RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12714
(117 letters)
>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 = 83.9 bits (208), Expect = 5e-23
Identities = 28/53 (52%), Positives = 36/53 (67%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C K VYP+E++ DGKLFH++CFRC+ C LR+ +Y G LYC PHF
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific
protein SF3. The first Lim domain of pollen specific
protein SF3: SF3 is a Lim protein that is found
exclusively in mature plant pollen grains. It contains
two LIM domains. The exact function of SF3 is unknown.
It may be a transcription factor required for the
expression of late pollen genes. It is possible that
SF3 protein is involved in controlling pollen-specific
processes such as male gamete maturation, pollen tube
formation, or even fertilization. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 63
Score = 74.0 bits (182), Expect = 6e-19
Identities = 26/57 (45%), Positives = 41/57 (71%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
C AC+K VY ++++ DG ++H++CFRC+ C L++ +Y+ G LYC PHF+QLF
Sbjct: 5 CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61
>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 = 69.8 bits (171), Expect = 2e-17
Identities = 24/61 (39%), Positives = 36/61 (59%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISR 94
C AC K VYP+EK+ +G +H++CF+C+ + +Y + G LYC H QLF +
Sbjct: 1 CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60
Query: 95 G 95
G
Sbjct: 61 G 61
>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 = 64.2 bits (157), Expect = 3e-15
Identities = 24/55 (43%), Positives = 37/55 (67%), Gaps = 2/55 (3%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMN--NGHLYCLPHF 87
C+ C K+VY +E++ +G FHR+CF+C+ C T LR+ +Y + +G YC PHF
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55
>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 = 62.1 bits (151), Expect = 2e-14
Identities = 21/53 (39%), Positives = 34/53 (64%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C +C K VY +E+I + ++H+ CFRC C L++++Y + G+LYC HF
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53
>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 = 58.3 bits (141), Expect = 5e-13
Identities = 23/53 (43%), Positives = 35/53 (66%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C K+VYP+E++ D + FH++CFRC C + L + +Y +G +YC PHF
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53
>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 = 57.8 bits (140), Expect = 1e-12
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTM--NNGHLYCLPH 86
C C K YP E ++ DG +H+ CF+C +C T L ++++T +G +YC H
Sbjct: 1 CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
>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 = 57.2 bits (138), Expect = 2e-12
Identities = 23/53 (43%), Positives = 37/53 (69%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C +C K VYPLE++ + +++H +CFRC+ C T L + +Y +G++YC PHF
Sbjct: 1 CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53
>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain,
containing two zinc fingers. LIM domains are
identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. LIM domains
are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. The consensus sequence of LIM
domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 53
Score = 55.8 bits (135), Expect = 5e-12
Identities = 16/53 (30%), Positives = 25/53 (47%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C K + E + GK +H CF+C+ C L +S+ +G YC +
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
>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 = 53.8 bits (129), Expect = 4e-11
Identities = 23/53 (43%), Positives = 31/53 (58%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C +C K VYP+E++ D +FH +CF C C L + SY +G YC PHF
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 50.8 bits (122), Expect = 6e-10
Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 35 CFACNKKVYPLEKIETD-GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
C C K +Y E + GK++H CFRC C L + +G LYC + +LF
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 50.5 bits (121), Expect = 6e-10
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 35 CFACNKKVYPLEKIET-DGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
C C K +Y E++ GK++H CF+C C L +++ +G LYC
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their
LIM, nebulin-like, and SH3 domains ,but differ
significantly at their linker regions. Both proteins
are ubiquitously expressed and involved in cytoskeletal
architecture, especially in the organization of focal
adhesions. LASP-1 and LASP-2, are important during
early embryo- and fetogenesis and are highly expressed
in the central nervous system of the adult. However,
only LASP-1 seems to participate significantly in
neuronal differentiation and plays an important
functional role in migration and proliferation of
certain cancer cells while the role of LASP-2 is more
structural. The expression of LASP-1 in breast tumors
is increased significantly. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 53
Score = 50.5 bits (121), Expect = 7e-10
Identities = 21/53 (39%), Positives = 29/53 (54%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C K VYP EK+ K++H+ CF+C C L M++Y N YC H+
Sbjct: 1 CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53
>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 = 49.3 bits (118), Expect = 2e-09
Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESY--TMNNGHLYCLPHF 87
C AC + V+ +++ DGKL+HR CFRC +C + L SY G C H
Sbjct: 1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55
>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 = 46.0 bits (110), Expect = 3e-08
Identities = 19/51 (37%), Positives = 30/51 (58%), Gaps = 4/51 (7%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTM--NNGHLYC 83
C C K VY E++ GK +H++CF C C R++S T+ ++G +YC
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNK--RLDSTTLAEHDGEIYC 49
>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 = 45.3 bits (107), Expect = 8e-08
Identities = 20/49 (40%), Positives = 26/49 (53%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY EKI GK +H+ CFRC +C L + +G +YC
Sbjct: 1 CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYC 49
>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 = 44.3 bits (104), Expect = 2e-07
Identities = 20/49 (40%), Positives = 25/49 (51%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C VY EKI GK +H+ CFRC +C L + T G +YC
Sbjct: 1 CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYC 49
>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 = 44.2 bits (104), Expect = 2e-07
Identities = 21/49 (42%), Positives = 26/49 (53%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY EK+ GK +H+ CFRC C L + T +G LYC
Sbjct: 1 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYC 49
>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 = 43.6 bits (103), Expect = 4e-07
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 33 SLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESY 74
C +C V+ E++ +GK++HR CF+C +C L S+
Sbjct: 3 EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSF 44
>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 = 41.9 bits (98), Expect = 1e-06
Identities = 21/53 (39%), Positives = 26/53 (49%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C K VYP EK+ K +H+ACF C C L M +Y YC H+
Sbjct: 1 CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53
>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 = 41.9 bits (98), Expect = 2e-06
Identities = 17/49 (34%), Positives = 28/49 (57%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C AC + VY E+++ DG+ FH+ CF C C L + +++ +YC
Sbjct: 2 CGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYC 50
>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 = 41.6 bits (98), Expect = 2e-06
Identities = 17/49 (34%), Positives = 25/49 (51%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY EK + G+ +H+ C RC +C L ++ + G YC
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYC 49
>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 = 40.7 bits (95), Expect = 4e-06
Identities = 17/49 (34%), Positives = 27/49 (55%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C AC K VY E+++ +G+ FH++CF C C L + + +YC
Sbjct: 1 CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYC 49
>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 = 40.6 bits (95), Expect = 5e-06
Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 1/55 (1%)
Query: 32 SSLCFACNKKVYP-LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLP 85
SS C AC K V P K+E +G+ +H CF C C + S+ + YC+P
Sbjct: 1 SSKCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVP 55
>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 = 39.7 bits (92), Expect = 1e-05
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C AC K VY E+I+ +G+ FH+ CF C C L + + +YC
Sbjct: 2 CGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYC 50
>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 = 38.7 bits (90), Expect = 2e-05
Identities = 18/49 (36%), Positives = 29/49 (59%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C+K+VY E++ + GK +HR C +C +C L S+ ++G YC
Sbjct: 1 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49
>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 = 38.7 bits (90), Expect = 2e-05
Identities = 18/52 (34%), Positives = 26/52 (50%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
C C VYP EKI + +H+ACF C C +L + ++ + YC H
Sbjct: 1 CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52
>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A.
The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A
belong to the CRP LIM domain protein family. The Mlp84B
protein contains five copies of the LIM domains, each
followed by a Glycin Rich Region (GRR). However, only
the first LIM domain of Mlp84B is in this family.
Mlp60A exhibits only one LIM domain linked to a
glycin-rich region. Mlp84B and Mlp60A are muscle
specific proteins and have been implicated in muscle
differentiation. While Mlp84B transcripts are enriched
at the terminal ends of muscle fibers, Mlp60A
transcripts are found throughout the muscle fibers. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 38.2 bits (89), Expect = 3e-05
Identities = 17/49 (34%), Positives = 24/49 (48%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY E+ G +H+ CF+C C +L + + G LYC
Sbjct: 2 CPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYC 50
>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein
(TLP). The first LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic
epithelial cells. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 37.6 bits (87), Expect = 6e-05
Identities = 18/49 (36%), Positives = 28/49 (57%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C+K VY EK+ + GK +HR C +C +C +L + ++G YC
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49
>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 = 37.7 bits (87), Expect = 6e-05
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY EK+ + G+ +HR C RC +C L + ++G YC
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
>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 = 37.3 bits (86), Expect = 9e-05
Identities = 16/49 (32%), Positives = 27/49 (55%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY E+++ +G+ FH++CF C C L + ++ +YC
Sbjct: 3 CGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYC 51
>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 = 36.7 bits (85), Expect = 2e-04
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 35 CFACNKKVYP-LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
C C K + + +E G ++H+ CF C+ C + +S+ YC+P ++ F
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma
subfamily with unknown function. The third LIM domain
of an Enigma subfamily with unknown function: The
Enigma LIM domain family is comprised of three
characterized members: Enigma, ENH, and Cypher
(mouse)/ZASP (human). These subfamily members contain a
single PDZ domain at the N-terminus and three LIM
domains at the C-terminus. They serve as adaptor
proteins, where the PDZ domain tethers the protein to
the cytoskeleton and the LIM domains, recruit signaling
proteins to implement corresponding functions. The
members of the enigma family have been implicated in
regulating or organizing cytoskeletal structure, as
well as involving multiple signaling pathways. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 35.2 bits (81), Expect = 5e-04
Identities = 16/56 (28%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 35 CFACNKKVYPLEK----IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
C +C +P+E +E +H CF CT+C L +S+ G +C H
Sbjct: 1 CVSCG---FPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLH 53
>gnl|CDD|188802 cd09418, LIM2_Prickle, The second LIM domain of Prickle. The
second LIM domain of Prickle: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle
1 and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle
2 is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 56
Score = 35.1 bits (81), Expect = 6e-04
Identities = 17/53 (32%), Positives = 26/53 (49%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C AC++ ++ E E +G+ +H F C +C L + Y M G YC F
Sbjct: 3 CSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCF 55
>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 = 35.1 bits (81), Expect = 7e-04
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 51 DGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
+ L+H ACFRC+ C +L +Y +++ +YC H+
Sbjct: 22 ESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
>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 = 35.0 bits (81), Expect = 7e-04
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C AC K + P K E GK +H CF C++C + +S+ + +YC+P +
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin. The first
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction
domain at the N-terminal. Testin is a cytoskeleton
associated focal adhesion protein that localizes along
actin stress fibers, at cell-cell-contact areas, and at
focal adhesion plaques. Testin interacts with a variety
of cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility
and adhesion events. Knockout mice experiments reveal
that tumor repressor function of Testin. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 35.1 bits (81), Expect = 7e-04
Identities = 16/35 (45%), Positives = 20/35 (57%)
Query: 53 KLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
KL+H ACF C+ C +L Y NG LYC H+
Sbjct: 24 KLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58
>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 = 34.7 bits (80), Expect = 8e-04
Identities = 18/50 (36%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 35 CFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY + + G L+H CF C C LR +++ NG +YC
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYC 50
>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 = 34.0 bits (78), Expect = 0.001
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C K+ + ++ + +H CFRC+ C L Y +G LYC +
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLS-NWYFEKDGKLYCRKDY 52
>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 = 0.001
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 55 FHRACFRCTQCCTVLRM-ESYTMNNGHLYCLPHF 87
FH CF C C L + + M +G +YC H+
Sbjct: 26 FHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
>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 = 34.2 bits (79), Expect = 0.001
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
K FH CF C C L + + G YC
Sbjct: 17 DKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYC 48
>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 = 33.7 bits (78), Expect = 0.002
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C AC++ ++ E + +GK +H F C QC L + Y + G YCL +
Sbjct: 3 CAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of
Four and a half LIM domains protein 2 (FHL2): FHL2 is
one of the best studied FHL proteins. FHL2 expression
is most abundant in the heart, and in brain, liver and
lung to a lesser extent. FHL2 participates in a wide
range of cellular processes, such as transcriptional
regulation, signal transduction, and cell survival by
binding to various protein partners. FHL2 has shown to
interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. Although FHL2 is abundantly
expressed in heart, the fhl2 null mice are viable and
had no detectable abnormal cardiac phenotype. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to s
upport the assembly of multimeric protein complexes.
Length = 57
Score = 33.5 bits (76), Expect = 0.003
Identities = 15/56 (26%), Positives = 28/56 (50%), Gaps = 1/56 (1%)
Query: 35 CFACNKKVYP-LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQ 89
C C K + P K+E G +H CF C +C + +S+ + +C+P +++
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEK 56
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture
of the actin cytoskeleton by regulating the activity of
the cofilin family proteins cofilin1, cofilin2, and
destrin. The mechanism of the activation is to
phosphorylates cofilin on serine 3 and inactivates its
actin-severing activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. LIMK1 is expressed in all tissues and is
localized to focal adhesions in the cell. LIMK1 can
form homodimers upon binding of HSP90 and is activated
by Rho effector Rho kinase and MAPKAPK2. LIMK1 is
important for normal central nervous system
development, and its deletion has been implicated in
the development of the human genetic disorder Williams
syndrome. Moreover, LIMK1 up-regulates the promoter
activity of urokinase type plasminogen activator and
induces its mRNA and protein expression in breast
cancer cells. The LIM domains have been shown to play
an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 74
Score = 33.7 bits (77), Expect = 0.003
Identities = 16/59 (27%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 29 GNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
GN +C +C + +Y + ++ +H CFRC +C L Y +G L+C +
Sbjct: 16 GNVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYE-KDGRLFCKKDY 73
>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 = 32.2 bits (74), Expect = 0.006
Identities = 10/48 (20%), Positives = 20/48 (41%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLY 82
C C ++ + G ++H CFRC C + ++++ Y
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
Score = 24.1 bits (53), Expect = 7.9
Identities = 7/26 (26%), Positives = 13/26 (50%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACF 60
C AC K + E + +H++C+
Sbjct: 28 CHACRKPIAEHEFSVSGNDPYHKSCY 53
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like
proteins: Ajuba like LIM protein family includes three
highly homologous proteins Ajuba, Limd1, and WTIP.
Members of the family contain three tandem C-terminal
LIM domains and a proline-rich N-terminal region. This
family of proteins functions as scaffolds,
participating in the assembly of numerous protein
complexes. In the cytoplasm, Ajuba binds Grb2 to
modulate serum-stimulated ERK activation. Ajuba also
recruits the TNF receptor-associated factor 6 (TRAF6)
to p62 and activates PKCKappa activity. Ajuba interacts
with alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 32.3 bits (74), Expect = 0.008
Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 4/53 (7%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMN-NGHLYCLP 85
C C + +E I + GK +H CFRC C L +T++ ++YC+
Sbjct: 1 CAVCGHLI--MEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVK 51
>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 = 32.1 bits (73), Expect = 0.009
Identities = 17/54 (31%), Positives = 24/54 (44%), Gaps = 1/54 (1%)
Query: 35 CFACNKKVYP-LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
CF C K + P K+E +G +H CF C C + + YC+P F
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPCF 54
>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 = 32.5 bits (74), Expect = 0.011
Identities = 19/66 (28%), Positives = 27/66 (40%), Gaps = 7/66 (10%)
Query: 22 EAPSNGTGNPSSLCFACNKKVYPLEKIETD----GKLFHRACFRCTQCCTVLRMESYTMN 77
+ P + LC C + PL + + G LFH CF C QC L+ + +
Sbjct: 21 DHPPAAEAATNELCGICGQ---PLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSL 77
Query: 78 NGHLYC 83
G YC
Sbjct: 78 EGKPYC 83
>gnl|CDD|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated
LIM protein) family. This family represents the LIM
domain of ALP (actinin-associated LIM protein) family.
Four proteins: ALP, CLP36, RIL, and Mystique have been
classified into the ALP subfamily of LIM domain
proteins. Each member of the subfamily contains an
N-terminal PDZ domain and a C-terminal LIM domain.
Functionally, these proteins bind to alpha-actinin
through their PDZ domains and bind or other signaling
molecules through their LIM domains. ALP proteins have
been implicated in cardiac and skeletal muscle
structure, function and disease, platelet, and
epithelial cell motility. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 31.2 bits (71), Expect = 0.016
Identities = 12/35 (34%), Positives = 14/35 (40%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
K H CF C C L+ + Y LYC H
Sbjct: 17 DKNRHPECFVCADCGLNLKNKGYFFIEDELYCETH 51
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 55
Score = 31.2 bits (71), Expect = 0.020
Identities = 14/51 (27%), Positives = 22/51 (43%), Gaps = 2/51 (3%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMN--NGHLYC 83
C C + + E G +H CF+C +C L +S + +G L C
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLSCDSNFLVLGDGSLIC 51
>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 30.8 bits (70), Expect = 0.024
Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 1/58 (1%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
C C + P EKI ++G+L+H CF C QC + G YC F+ LF
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLF 58
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain,
and a short consensus C-terminal region. It is the
smallest molecule in the ALP LIM domain containing
protein family. RIL was identified in rat fibroblasts
and in human lymphocytes. The LIM domain interacts with
the AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 30.7 bits (69), Expect = 0.027
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 53 KLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFK 88
KL+H CF C C L+ Y + LYC H K
Sbjct: 18 KLYHPECFMCDDCGLNLKQRGYFFIDEQLYCETHAK 53
>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP,
actinin-associated LIM protein. This family represents
the LIM domain of ALP, actinin-associated LIM protein.
ALP contains an N-terminal PDZ domain, a C-terminal LIM
domain and an ALP-subfamily-specific 34-amino-acid
motif termed ALP-like motif (AM), which contains a
putative consensus protein kinase C (PKC)
phosphorylation site and two alpha-helices. ALP
proteins are found in heart and in skeletal muscle. ALP
may act as a signaling molecule which is regulated by
PKC-dependent signaling. ALP plays an essential role in
the development of RV (right ventricle) chamber. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 30.6 bits (69), Expect = 0.030
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 53 KLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
K H CF C+ C L+ + Y G LYC H
Sbjct: 18 KYRHPECFVCSDCNLNLKQKGYFFVEGQLYCEAH 51
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein
family, which comprises LIMK1 and LIMK2. LIMK contains
two LIM domains, a PDZ domain, and a kinase domain.
LIMK is involved in the regulation of actin
polymerization and microtubule disassembly. LIMK
influences architecture of the actin cytoskeleton by
regulating the activity of the cofilin family proteins
cofilin1, cofilin2, and destrin. The mechanism of the
activation is to phosphorylates cofilin on serine 3 and
inactivates its actin-severing activity, altering the
rate of actin depolymerization. LIMK activity is
activated by phosphorylation of a threonine residue
within the activation loop of the kinase by
p21-activated kinases 1 and 4 and by Rho kinase. LIMKs
can function in both cytoplasm and nucleus. Both LIMK1
and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is
expressed in all tissues. While LIMK1 localizes mainly
at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 30.6 bits (69), Expect = 0.033
Identities = 14/53 (26%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C ++ + +H +CF+C+ C +L Y +G LYC H+
Sbjct: 1 CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL-TNWYYEKDGKLYCHKHY 52
>gnl|CDD|216792 pfam01927, DUF82, Protein of unknown function DUF82. This
prokaryotic protein family has no known function. The
protein contains four conserved cysteines that may be
involved in metal binding or disulphide bridges.
Length = 146
Score = 31.8 bits (73), Expect = 0.038
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 6/39 (15%)
Query: 33 SLCFACNKKVYPLEKIETDGKL------FHRACFRCTQC 65
S C CN + P+ K E G++ + +RC +C
Sbjct: 91 SRCLKCNGPLEPVSKEEVAGRVPPYVYERYDEFWRCPKC 129
>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 = 30.1 bits (68), Expect = 0.042
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 55 FHRACFRCTQCCTVLRM-ESYTMNNGHLYCLPHF 87
+H ACF C C L E + + + C H+
Sbjct: 22 YHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga
GTPase-Activating Proteins. The second LIM domain of
Rga GTPase-Activating Proteins: The members of this
family contain two tandem repeats of LIM domains and a
Rho-type GTPase activating protein (RhoGap) domain. Rga
activates GTPases during polarized morphogenesis. In
yeast, a known regulating target of Rga is CDC42p, a
small GTPase. The LIM domain is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 30.1 bits (68), Expect = 0.051
Identities = 12/50 (24%), Positives = 21/50 (42%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCL 84
C C KK+ + + + + CFRC +C + Y L+C+
Sbjct: 1 CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRGLFCM 50
>gnl|CDD|221188 pfam11725, AvrE, Pathogenicity factor. This family is secreted by
gram-negative Gammaproteobacteria such as Pseudomonas
syringae of tomato and the fire blight plant pathogen
Erwinia amylovora, amongst others. It is an essential
pathogenicity factor of approximately 198 kDa. Its
injection into the host-plant is dependent upon the
bacterial type III or Hrp secretion system. The family
is long and carries a number of predicted functional
regions, including an ERMS or endoplasmic reticulum
membrane retention signal at both the C- and the
N-termini, a leucine-zipper motif from residues 539-560,
and a nuclear localisation signal at 1358-1361. this
conserved AvrE-family of effectors is among the few that
are required for full virulence of many phytopathogenic
pseudomonads, erwinias and pantoeas.
Length = 1771
Score = 31.3 bits (71), Expect = 0.081
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 9/43 (20%)
Query: 74 YTMN-NGHLYCLPHFKQLFISRGNYDEGFGSDQHKRKWQPVAT 115
Y + G L+ +P R ++ G SD+ K KWQ +A
Sbjct: 756 YALTSTGELFFMP--------REDWQNGASSDKMKAKWQKLAL 790
>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 = 29.3 bits (66), Expect = 0.083
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNN-GHLYCLPHF 87
GK +H CF C C + ES+ ++ +YCL +
Sbjct: 17 GKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
>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 = 29.5 bits (67), Expect = 0.085
Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 4/57 (7%)
Query: 35 CFACNKKVYPLEKIETDGKL---FHRACFRCTQC-CTVLRMESYTMNNGHLYCLPHF 87
C C ++ DG+L +HR CF CT C C + + YC H+
Sbjct: 1 CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>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 = 0.093
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCL 84
K +H CF+C +C VL E Y +G YC
Sbjct: 18 DKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCE 49
>gnl|CDD|223297 COG0219, CspR, Predicted rRNA methylase (SpoU class) [Translation,
ribosomal structure and biogenesis].
Length = 155
Score = 30.6 bits (70), Expect = 0.10
Identities = 24/102 (23%), Positives = 41/102 (40%), Gaps = 13/102 (12%)
Query: 14 VKIILNQPEAPSNGTGNPSSLCFACNKKVYPLEKI--ETDGKLFHRACFRCTQCCTVLRM 71
+ I+L QPE P N TGN C A +++ +E + + D K RA + ++
Sbjct: 3 LNIVLYQPEIPPN-TGNIIRTCAATGAELHLIEPLGFDLDDKRLKRAGLDYHEKASLTEH 61
Query: 72 ESYT------MNNGHLYCLPHFKQLFISRGNYDEG----FGS 103
+S G L+ L + ++ +G FG
Sbjct: 62 DSLEAFLEAEPIGGRLFALTTKGTTTYTDVSFQKGDYLLFGP 103
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated
in roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 29.1 bits (65), Expect = 0.11
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
G +H CF+C C +L Y +G +YC H
Sbjct: 23 GACWHPQCFQCASCQELLVDLIYFYQDGKIYCGRH 57
>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 = 28.9 bits (65), Expect = 0.11
Identities = 10/36 (27%), Positives = 15/36 (41%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
G+ +H F C+ C L + G LYC +
Sbjct: 17 GRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 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 = 29.0 bits (65), Expect = 0.11
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVL-RMESYTMNNGHLYC 83
C AC + + E + G ++H CF C+ C L + + NG L+C
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion
events. Prickles have been implicated in roles of
regulating tissue polarity or planar cell polarity
(PCP). Dyxin involves in lung and heart development by
interaction with GATA6 and blocking GATA6 activated
target genes. LIMPETin might be the recombinant product
of genes coding testin and four and half LIM proteins
and its function is not well understood. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 57
Score = 29.3 bits (66), Expect = 0.11
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 3/54 (5%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRA---CFRCTQCCTVLRMESYTMNNGHLYCLP 85
C AC + + P + A CF C+ C L + + NG ++C P
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFCSP 54
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 29.0 bits (65), Expect = 0.13
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C+KK+ E + + +H +CF C C + + M +G YC
Sbjct: 1 CARCHKKILG-EVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYC 48
>gnl|CDD|211559 TIGR00185, tRNA_yibK_trmL, tRNA
(cytidine(34)-2'-O)-methyltransferase. TrmL
(previously YibK) is responsible for 2'-O-methylation
at tRNA(Leu) position 34 [Protein synthesis, tRNA and
rRNA base modification].
Length = 153
Score = 30.5 bits (69), Expect = 0.13
Identities = 17/64 (26%), Positives = 30/64 (46%), Gaps = 3/64 (4%)
Query: 13 AVKIILNQPEAPSNGTGNPSSLCFACNKKVYPLEKI--ETDGKLFHRACFRCTQCCTVLR 70
+ I+L +PE P N TGN + C A +++ +E + D K RA + +
Sbjct: 1 MLNIVLYEPEIPPN-TGNIARTCAATGTRLHLIEPLGFFLDDKRLKRAGLDYWEFVQLFY 59
Query: 71 MESY 74
+S+
Sbjct: 60 HKSW 63
>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 = 28.6 bits (64), Expect = 0.15
Identities = 12/41 (29%), Positives = 24/41 (58%)
Query: 45 LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLP 85
++K+E G+ +H CF C +C + +S+ + +YC+P
Sbjct: 12 MKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVP 52
>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 = 28.6 bits (64), Expect = 0.18
Identities = 12/45 (26%), Positives = 19/45 (42%), Gaps = 7/45 (15%)
Query: 46 EKIETDGK-------LFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
+KI D K +H CF+C +C L + + + L C
Sbjct: 10 KKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLC 54
>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 = 28.5 bits (64), Expect = 0.20
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQC 65
C +C V E + GK +H CF C+ C
Sbjct: 4 CDSCQDFVEG-EVVSALGKTYHPKCFVCSVC 33
>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred
partner (LPP). The first LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at
the N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of
cell adhesion, cell-cell contacts and transiently in
the nucleus. In nucleus, it acts as a coactivator for
the ETS domain transcription factor PEA3. In addition
to PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and
vasodilator- stimulated phosphoprotein (VASP), has a
weak targeting capacity. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 54
Score = 28.2 bits (63), Expect = 0.21
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 9/54 (16%)
Query: 35 CFACNKKVYPLEKIETDG-----KLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C +KV E G +++H +CF C QC L+ + + +G YC
Sbjct: 1 CVKCGEKVLG----EGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYC 50
>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 = 28.3 bits (64), Expect = 0.23
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 53 KLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
+H CF C C +L Y ++G +YC H+
Sbjct: 24 ACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
>gnl|CDD|183930 PRK13264, PRK13264, 3-hydroxyanthranilate 3,4-dioxygenase;
Provisional.
Length = 177
Score = 29.5 bits (67), Expect = 0.24
Identities = 16/46 (34%), Positives = 18/46 (39%), Gaps = 14/46 (30%)
Query: 35 CFACNKKVY----PLEKIETD-GKLFHRACF-------RCTQCCTV 68
C CN KV+ L IETD +F F C C TV
Sbjct: 123 CDECNHKVHEVEVQLTDIETDLPPVFAA--FYASEELRTCDNCGTV 166
>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 = 28.1 bits (63), Expect = 0.24
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVL-RMESYTMNNGHLYC 83
C C + + ++ G+ +H +C RC C T L R S + +YC
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYC 50
>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 = 28.2 bits (63), Expect = 0.25
Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 1/53 (1%)
Query: 35 CFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
C C+ + ++ +E G +H CF C C L +++ C H
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNH 53
>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma. The
second LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes, such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 28.0 bits (62), Expect = 0.26
Identities = 16/49 (32%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C KK+ E + +H CF C C T +R ++ M G YC
Sbjct: 1 CAKCKKKITG-EIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYC 48
>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 = 28.2 bits (63), Expect = 0.26
Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 3/52 (5%)
Query: 35 CFACNKKVYPL---EKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C AC K + + + I + + +H CF C C T L + + + G + C
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 28.0 bits (62), Expect = 0.32
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 55 FHRACFRCTQCCTVLRMESYTMNNGHLYC 83
+H CFRC +C L E +T + L C
Sbjct: 26 YHEHCFRCFRCDRSLADEPFTCQDEELLC 54
>gnl|CDD|151819 pfam11379, DUF3182, Protein of unknown function (DUF3182). This
family of proteins with unknown function appears to be
restricted to Proteobacteria.
Length = 355
Score = 29.6 bits (67), Expect = 0.32
Identities = 10/23 (43%), Positives = 11/23 (47%)
Query: 86 HFKQLFISRGNYDEGFGSDQHKR 108
+ LF SR NYD G D R
Sbjct: 261 CYPGLFASRRNYDVAQGLDAEGR 283
>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 = 28.2 bits (63), Expect = 0.33
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 12/60 (20%)
Query: 35 CFACNKKVYPLE------KIETDGKLFHRACFRCTQCCTVLRMES-----YTMNNGHLYC 83
C C + + P +I + FH C++C C +L E Y + +GHL C
Sbjct: 1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPL-DGHLLC 59
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated
protein-protein interactions. PINCH comprises an array
of five LIM domains that interact with integrin-linked
kinase (ILK), Nck2 (also called Nckbeta or Grb4) and
other interaction partners. These interactions are
essential for triggering the FA assembly and for
relaying diverse mechanical and biochemical signals
between Cell-extracellular matrix and the actin
cytoskeleton. The PINCH LIM4 domain recognizes the
third SH3 domain of another adaptor protein, Nck2. This
step is an important component of integrin signaling
event. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assem bly of multimeric
protein complexes.
Length = 54
Score = 27.7 bits (62), Expect = 0.34
Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 1/55 (1%)
Query: 33 SLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
+C AC + + + GK +H F C +C + G YC H+
Sbjct: 1 PICGACRRPIEG-RVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
>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 = 28.0 bits (62), Expect = 0.34
Identities = 15/61 (24%), Positives = 30/61 (49%), Gaps = 2/61 (3%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHL-YCLPHFKQLFIS 93
C C++K+ ++ GK +H CF C C L ES+ ++ + +C+ + + +
Sbjct: 1 CAVCDQKITD-RMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAP 59
Query: 94 R 94
R
Sbjct: 60 R 60
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 27.7 bits (61), Expect = 0.34
Identities = 14/49 (28%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C +K+ E I + +H +CF C C +R + + +G YC
Sbjct: 1 CGRCQRKILG-EVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYC 48
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of
Four and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth,
differentiation, and sarcomere assembly by acting as a
modulator of transcription factors. Defects in FHL1
gene are responsible for a number of Muscular
dystrophy-like muscle disorders. It has been detected
that FHL1 binds to Myosin-binding protein C, regulating
myosin filament formation and sarcomere assembly. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 64
Score = 27.8 bits (62), Expect = 0.35
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 51 DGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
+G +H CF C +C L + + +NG +YC
Sbjct: 25 EGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at
the N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of
cell adhesion, cell-cell contacts and transiently in
the nucleus. In nucleus, it acts as a coactivator for
the ETS domain transcription factor PEA3. In addition
to PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and
vasodilator- stimulated phosphoprotein (VASP), has a
weak targeting capacity. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 60
Score = 27.9 bits (62), Expect = 0.38
Identities = 18/62 (29%), Positives = 30/62 (48%), Gaps = 4/62 (6%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMN-NGHLYCLPHFKQLFI 92
C C+K + L++I GK +H CF C C L +T++ ++C+ F + F
Sbjct: 1 CSVCSKPI--LDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFA 58
Query: 93 SR 94
R
Sbjct: 59 PR 60
>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 = 27.7 bits (62), Expect = 0.41
Identities = 11/31 (35%), Positives = 17/31 (54%), Gaps = 3/31 (9%)
Query: 55 FHRACFRCTQCCTVLRMESYT--MNNGHLYC 83
+H AC +C +C L E+ T + +G YC
Sbjct: 22 WHAACLKCAECGQYL-DETCTCFVRDGKTYC 51
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog
(ENH) family. The third LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 27.2 bits (60), Expect = 0.53
Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 35 CFACNKKVYPLEK----IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
C C +P+E +E G +H CF C+ CC L +++ C H
Sbjct: 1 CHGCE---FPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKH 53
>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 = 27.3 bits (61), Expect = 0.53
Identities = 13/37 (35%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 52 GKLFHRACFRCTQCCTVLRM-ESYTMNNGHLYCLPHF 87
G+ +H F C+ C TV +SY + G +YC H+
Sbjct: 17 GRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 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 = 27.4 bits (60), Expect = 0.58
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 54 LFHRACFRCTQCCTVLRM-ESYTMNNGHLYCLPHF 87
++H +CF CT C L + + M + +YC HF
Sbjct: 25 VYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59
>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The first LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved
in actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic
acid (LPA)-induced cell migration. TRIP6 can shuttle to
the nucleus to serve as a coactivator of AP-1 and
NF-kappaB transcriptional factors. Moreover, TRIP6 can
form a ternary complex with the NHERF2 PDZ protein and
LPA2 receptor to regulate LPA-induced activation of ERK
and AKT, rendering cells resistant to chemotherapy.
Recent evidence shows that TRIP6 antagonizes
Fas-Induced apoptosis by enhancing the antiapoptotic
effect of LPA in cells. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 54
Score = 27.0 bits (60), Expect = 0.66
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 53 KLFHRACFRCTQCCTVLRMESYTMNNGHLYCLP 85
++FH CF C C LR + + YC P
Sbjct: 20 QVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEP 52
>gnl|CDD|188815 cd09431, LIM3_Fhl2, The third LIM domain of Four and a half LIM
domains protein 2 (FHL2). The third LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one
of the best studied FHL proteins. FHL2 expression is
most abundant in the heart, and in brain, liver and
lung to a lesser extent. FHL2 participates in a wide
range of cellular processes, such as transcriptional
regulation, signal transduction, and cell survival by
binding to various protein partners. FHL2 has shown to
interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. Although FHL2 is abundantly
expressed in heart, the fhl2 null mice are viable and
had no detectable abnormal cardiac phenotype. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to s
upport the assembly of multimeric protein complexes.
Length = 57
Score = 26.9 bits (59), Expect = 0.69
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 55 FHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
+H+ CF CT C L + +T + YCL F L+
Sbjct: 20 WHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLY 56
>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain
only protein 2). The second LIM domain of LMO2 (LIM
domain only protein 2): LMO2 is a nuclear protein that
plays important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex
that is capable of transcriptional activation. LMOs
have also been shown to be involved in oncogenesis.
LMO1 and LMO2 are activated in T-cell acute
lymphoblastic leukemia by distinct chromosomal
translocations. LMO2 was also shown to be involved in
erythropoiesis and is required for the hematopoiesis in
the adult animals. All LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 26.9 bits (59), Expect = 0.73
Identities = 10/32 (31%), Positives = 18/32 (56%), Gaps = 1/32 (3%)
Query: 35 CFACNKKVYPLE-KIETDGKLFHRACFRCTQC 65
C +C+K++ E + K++H CF+C C
Sbjct: 1 CASCDKRIRAYEMTMRVKDKVYHLECFKCAAC 32
>gnl|CDD|200935 pfam00022, Actin, Actin.
Length = 367
Score = 28.3 bits (64), Expect = 0.78
Identities = 9/29 (31%), Positives = 17/29 (58%), Gaps = 2/29 (6%)
Query: 81 LYCLPHFKQLFISRGNYDEGFGSDQ-HKR 108
L L F+Q+++S+ Y+E GS ++
Sbjct: 338 LASLGTFQQMWVSKQEYEE-HGSSVVERK 365
>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 = 27.0 bits (59), Expect = 0.85
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 54 LFHRACFRCTQCCTVLRM-ESYTMNNGHLYCLPHF 87
++H CF CT C +L + + M + +YC HF
Sbjct: 25 VYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59
>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 = 26.6 bits (59), Expect = 0.87
Identities = 9/32 (28%), Positives = 15/32 (46%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
+ +H CFRC +C L E + + + C
Sbjct: 19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILC 50
>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 = 26.8 bits (59), Expect = 0.89
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMN-NGHLYCLPHF 87
C C+K + +E+I GK +H CF C C L +T++ G ++C+ F
Sbjct: 1 CSVCSKPI--MERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM
(abLIM) proteins. The fourth LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to
function as a tumor suppressor. AbLIM-2 and -3, mainly
expressed in muscle and neuronal tissue, bind to
F-actin strongly. They may serve as a scaffold for
signaling modules of the actin cytoskeleton and thereby
modulate transcription. It has shown that LIM domains
of abLIMs interact with STARS (striated muscle
activator of Rho signaling), which directly binds actin
and stimulates serum-response factor (SRF)-dependent
transcription. All LIM domains are 50-60 amino acids in
size and share two characteristic highly conserved zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 26.6 bits (59), Expect = 1.0
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 9/36 (25%)
Query: 35 CFACNK----KVYPLEKIETDGKLFHRACFRCTQCC 66
C AC+K KV +E GK +H C RC++C
Sbjct: 1 CEACDKFITGKV-----LEAGGKHYHPTCARCSRCG 31
>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 = 26.4 bits (58), Expect = 1.3
Identities = 14/51 (27%), Positives = 23/51 (45%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLP 85
C C++ ++ E + + + +H F C C +L E Y M N C P
Sbjct: 3 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKP 53
>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2. The first LIM
domain of Lhx2: Lhx2 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. The Lhx2 protein has been shown
to bind to the mouse M71 olfactory receptor promoter.
Similar to other LIM domains, this domain family is
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 64
Score = 26.5 bits (58), Expect = 1.4
Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 1/57 (1%)
Query: 28 TGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMN-NGHLYC 83
+ + ++LC C K+ + K +H C +C +C L E + +G +YC
Sbjct: 4 SSDRAALCAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYC 60
>gnl|CDD|144537 pfam00979, Reovirus_cap, Reovirus outer capsid protein, Sigma 3.
Sigma 3 is the major outer capsid protein of reovirus.
Sigma 3 is encoded by genome segment 4. Sigma 3 binds
to double stranded RNA and associates with polypeptide
u1 and its cleavage product u1C to form the outer shell
of the virion. The Sigma 3 protein possesses a
zinc-finger motif and an RNA-binding domain in the N
and C termini respectively. This protein is also
thought to play a role in pathogenesis.
Length = 367
Score = 27.9 bits (62), Expect = 1.4
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 3/27 (11%)
Query: 62 CTQCCTVLRMESYTMNNGHLYCLPHFK 88
C+QCC VL + + L PH +
Sbjct: 51 CSQCCGVLYYGALPRD---LNYFPHHR 74
>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 = 25.9 bits (57), Expect = 1.4
Identities = 15/49 (30%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C CNK + + + +HR CF CT C L + +T + YC
Sbjct: 1 CSKCNK-IINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in
tandem and an N-terminal single zinc finger domain with
a consensus sequence equivalent to the C-terminal half
of a LIM domain. LIMPETin is an exception, containing
six LIM domains. FHL1, 2 and 3 are predominantly
expressed in muscle tissues, and FHL5 is highly
expressed in male germ cells. FHL proteins exert their
roles as transcription co-activators or co-repressors
through a wide array of interaction partners. For
example, FHL1 binds to Myosin-binding protein C,
regulating myosin filament formation and sarcomere
assembly. FHL2 has shown to interact with more than 50
different proteins, including receptors, structural
proteins, transcription factors and cofactors, signal
transducers, splicing factors, DNA replication and
repair enzymes, and metabolic enzymes. FHL3 int eracts
with many transcription factors, such as CREB,
BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 25.8 bits (57), Expect = 1.6
Identities = 14/50 (28%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCL 84
C C KK + + +H+ CF CT C L + +T + + YC+
Sbjct: 1 CAKC-KKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCV 49
>gnl|CDD|234157 TIGR03287, methan_mark_16, putative methanogenesis marker 16
metalloprotein. Members of this protein family, to
date, are found in a completed prokaryotic genome if and
only if the species is one of the archaeal methanogens.
The exact function is unknown, but likely is linked to
methanogenesis or a process closely connected to it.
This protein is a predicted to bind FeS clusters, based
on the presence of two copies of the Fer4 domain
(pfam00037), with each copy having four Cys residues
invariant across all members [Energy metabolism,
Methanogenesis].
Length = 391
Score = 27.4 bits (61), Expect = 1.7
Identities = 13/50 (26%), Positives = 21/50 (42%), Gaps = 1/50 (2%)
Query: 35 CFACNKKVY-PLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C + P+ I+ DG L CF C C + ++ +N G +
Sbjct: 307 CDPCLVEEACPVPAIKKDGTLNTEDCFGCGYCAEICPGGAFEVNLGSVRV 356
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one
of the best studied FHL proteins. FHL2 expression is
most abundant in the heart, and in brain, liver and
lung at lesser extent. FHL2 participates in a wide
range of cellular processes, such as transcriptional
regulation, signal transduction, and cell survival by
binding to various protein partners. FHL2 has shown to
interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. Although FHL2 is abundantly
expressed in heart, the fhl2 null mice are viable and
had no detectable abnormal cardiac phenotype. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 62
Score = 26.0 bits (57), Expect = 1.7
Identities = 14/53 (26%), Positives = 23/53 (43%), Gaps = 1/53 (1%)
Query: 32 SSLCFACNKKV-YPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
S+ C C K + + + + +H +CF C QC L + + HL C
Sbjct: 2 SNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 54
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4
family. The second LIM domain of Lhx3-Lhx4 family:
Lhx3 and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
The LHX3 and LHX4 LIM-homeodomain transcription factors
play essential roles in pituitary gland and nervous
system development. Although LHX3 and LHX4 share marked
sequence homology, the genes have different expression
patterns. They play overlapping, but distinct functions
during the establishment of the specialized cells of
the mammalian pituitary gland and the nervous system.
Lhx3 proteins have been demonstrated the ability to
directly bind to the promoters/enhancers of several
pituitary hormone gene promoters to cause increased
transcription.Lhx3a and Lhx3b, whose mRNAs have
distinct temporal expression profiles during
development, are two isoforms of Lhx3. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 56
Score = 25.8 bits (57), Expect = 1.9
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 3/52 (5%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRM--ESYTMNNGHLYC 83
C C++ + P + + ++H CF C C L E Y M + L C
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVC 52
>gnl|CDD|188822 cd09438, LIM3_Ajuba_like, The third LIM domain of Ajuba-like
proteins. The third LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate
serum-stimulated ERK activation. Ajuba also recruits
the TNF receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 62
Score = 25.8 bits (57), Expect = 2.2
Identities = 18/59 (30%), Positives = 24/59 (40%), Gaps = 11/59 (18%)
Query: 35 CFACNKKVYPLEKIETD------GKLFHRACFRCTQCCTVLRMES----YTMNNGHLYC 83
C AC + + P E E K +H C+ C C L E Y + +GHL C
Sbjct: 1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRCYPL-DGHLLC 58
>gnl|CDD|188833 cd09449, LIM_Mystique, The LIM domain of Mystique, a subfamily of
ALP LIM domain proteins. The LIM domain of Mystique, a
subfamily of ALP LIM domain proteins: Mystique is the
most recently identified member of the ALP protein
family. It also interacts with alpha-actinin, as other
ALP proteins do. Mystique promotes cell attachment and
migration and suppresses anchorage-independent growth.
The LIM domain of Mystique is required for the
suppression function. Moreover, Mystique functions as
an ubiquitin E3 ligase acting on STAT proteins to cause
their proteosome mediated degradation. As in all LIM
domains, this 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
complexes.
Length = 53
Score = 25.6 bits (56), Expect = 2.3
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 50 TDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
+G+ H C+ CT C L+M + ++C H
Sbjct: 16 QEGRYRHPGCYTCTDCGLNLKMRGHFWAGEKMFCEKH 52
>gnl|CDD|173506 PTZ00281, PTZ00281, actin; Provisional.
Length = 376
Score = 27.0 bits (59), Expect = 2.4
Identities = 11/28 (39%), Positives = 17/28 (60%)
Query: 81 LYCLPHFKQLFISRGNYDEGFGSDQHKR 108
L L F+Q++IS+ YDE S H++
Sbjct: 347 LASLSTFQQMWISKEEYDESGPSIVHRK 374
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The
first LIM domain of Prickle: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 25.7 bits (57), Expect = 2.5
Identities = 12/31 (38%), Positives = 16/31 (51%)
Query: 56 HRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
H ACF C+ C +L Y +G +YC H
Sbjct: 27 HPACFVCSTCKELLVDLIYFYQDGKVYCGRH 57
>gnl|CDD|212667 cd10170, HSP70_NBD, Nucleotide-binding domain of the HSP70
family. HSP70 (70-kDa heat shock protein) family
chaperones assist in protein folding and assembly and
can direct incompetent "client" proteins towards
degradation. Typically, HSP70s have a
nucleotide-binding domain (NBD) and a substrate-binding
domain (SBD). The nucleotide sits in a deep cleft
formed between the two lobes of the NBD. The two
subdomains of each lobe change conformation between
ATP-bound, ADP-bound, and nucleotide-free states. ATP
binding opens up the substrate-binding site;
substrate-binding increases the rate of ATP hydrolysis.
HSP70 chaperone activity is regulated by various
co-chaperones: J-domain proteins and nucleotide
exchange factors (NEFs). Some HSP70 family members are
not chaperones but instead, function as NEFs to remove
ADP from their HSP70 chaperone partners during the ATP
hydrolysis cycle, some may function as both chaperones
and NEFs.
Length = 369
Score = 26.8 bits (60), Expect = 3.0
Identities = 12/38 (31%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 8 TSSKIAVKIILNQPEAPSNGTGN---PSSLCFACNKKV 42
T+S +A +PE NG G+ PS + F + +V
Sbjct: 8 TNSAVAYVDNGGKPEIIPNGEGSRTTPSVVYFDGDGEV 45
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 25.3 bits (55), Expect = 3.0
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
G +H CF C+ C +L Y +G +YC H
Sbjct: 23 GVCWHPQCFVCSVCNELLVDLIYFYQDGKIYCGRH 57
>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 = 25.1 bits (55), Expect = 3.1
Identities = 12/52 (23%), Positives = 25/52 (48%), Gaps = 3/52 (5%)
Query: 35 CFACNKKVYPL---EKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C ACNK + + + + + +H+ CF+C++C L + + + C
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILC 52
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 24.9 bits (54), Expect = 3.3
Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 3/50 (6%)
Query: 35 CFACNKKVYPLEKIETD-GKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C+ CN + L+K+ T + +H F C QC E + +G YC
Sbjct: 1 CYYCNGPI--LDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYC 48
>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin. The
third LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 25.2 bits (55), Expect = 3.4
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 54 LFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
L+H CF C +C T S+ ++G YC H+
Sbjct: 19 LWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6. The second
LIM domain of Lhx6. Lhx6 is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Lhx6 functions in brain and nervous system. It is
expressed at high levels in several regions of the
embryonic mouse CNS, including the telencephalon and
hypothalamus, and the first branchial arch. Lhx6 is
proposed to have a role in patterning of the mandible
and maxilla, and in signaling during odontogenesis. In
brain sections, knockdown of Lhx6 gene blocks the
normal migration of neurons to the cortex. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 25.0 bits (54), Expect = 3.5
Identities = 10/32 (31%), Positives = 16/32 (50%), Gaps = 1/32 (3%)
Query: 35 CFACNKKVYPLEKIE-TDGKLFHRACFRCTQC 65
C C +++Y + + G +H ACF C C
Sbjct: 1 CARCGRQIYASDWVRRARGNAYHLACFACFSC 32
>gnl|CDD|214592 smart00268, ACTIN, Actin. ACTIN subfamily of
ACTIN/mreB/sugarkinase/Hsp70 superfamily.
Length = 373
Score = 26.5 bits (59), Expect = 3.5
Identities = 9/26 (34%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 84 LPHFKQLFISRGNYDEGFGSDQHKRK 109
L F+ ++I++ Y+E GS +RK
Sbjct: 347 LSTFEDMWITKKEYEE-SGSQIVERK 371
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. In mouse, mutations in Lmx1a result in
failure of the roof plate to develop. Lmx1a may act
upstream of other roof plate markers such as MafB,
Gdf7, Bmp6, and Bmp7. Further characterization of these
mice reveals numerous defects including disorganized
cerebellum, hippocampus, and cortex; altered
pigmentation; female sterility, skeletal defects, and
behavioral abnormalities. In the mouse, Lmx1b
functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 25.1 bits (55), Expect = 3.7
Identities = 14/51 (27%), Positives = 23/51 (45%), Gaps = 2/51 (3%)
Query: 35 CFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRM-ESYTMNNGHLYC 83
C C +K+ P E + ++H CF C C L+ + + + G L C
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLC 51
>gnl|CDD|132910 cd07032, RNAP_I_II_AC40, AC40 subunit of Eukaryotic RNA polymerase
(RNAP) I and RNAP III. The eukaryotic AC40 subunit of
RNA polymerase (RNAP) I and RNAP III is involved in the
assembly of RNAP subunits. RNAP is a large multi-subunit
complex responsible for the synthesis of RNA. It is the
principal enzyme of the transcription process, and is a
final target in many regulatory pathways that control
gene expression in all living cells. At least three
distinct RNAP complexes are found in eukaryotic nuclei:
RNAP I, RNAP II, and RNAP III. RNAP I is responsible for
the synthesis of ribosomal RNA precursor, while RNAP III
functions in the synthesis of 5S and tRNA. The AC40
subunit is the equivalent of the RPB3 subunit of RNAP
II. The RPB3 subunit is similar to the bacterial RNAP
alpha subunit in that it contains two subdomains: one
subdomain is similar the eukaryotic Rpb11/AC19/archaeal
L subunit which is involved in dimerization; and the
other is an inserted beta sheet subdomain. The RPB3
subunit heterodimerizes with the RPB11 subunit, and
together with RPB10 and RPB12, anchors the two largest
subunits, RPB1 and RPB2, and stabilizes their
association. The homology of AC40 to RPB3 suggests a
similar function. The AC40 subunit is likely to
associate with the RPB11 counterpart, AC19, to form a
heterodimer, which stabilizes the association of the two
largest subunits of RNAP I and RNAP III.
Length = 291
Score = 26.4 bits (59), Expect = 3.7
Identities = 10/17 (58%), Positives = 11/17 (64%), Gaps = 2/17 (11%)
Query: 100 GFGSDQHKRKWQPVATA 116
G G D H K+ PVATA
Sbjct: 169 GIGKD-HA-KFSPVATA 183
>gnl|CDD|198277 cd10414, SH2_Grb14, Src homology 2 (SH2) domain found in the growth
factor receptor bound, subclass 14 (Grb14) proteins.
The Grb family binds to the epidermal growth factor
receptor (EGFR, erbB1) via their SH2 domains. Grb14 is
part of the Grb7 family of proteins which also includes
Grb7, and Grb14. They are composed of an N-terminal
Proline-rich domain, a Ras Associating-like (RA) domain,
a Pleckstrin Homology (PH) domain, a phosphotyrosine
interaction region (PIR, BPS) and a C-terminal SH2
domain. The SH2 domains of Grb7, Grb10 and Grb14
preferentially bind to a different RTK. Grb14 binds to
Fibroblast Growth Factor Receptor (FGFR) and weakly to
the erbB2 receptor. In general SH2 domains are involved
in signal transduction. They typically bind
pTyr-containing ligands via two surface pockets, a pTyr
and hydrophobic binding pocket, allowing proteins with
SH2 domains to localize to tyrosine phosphorylated
sites.
Length = 108
Score = 26.0 bits (57), Expect = 3.7
Identities = 17/57 (29%), Positives = 29/57 (50%), Gaps = 2/57 (3%)
Query: 33 SLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRM-ESYTMNNGHLYC-LPHF 87
S+ K + + +E DG+LFH T+ ++++ E Y +N G L C L H+
Sbjct: 46 SMSHGQKIKHFQIIPVEDDGELFHTLDDGHTRFTDLIQLVEFYQLNKGVLPCKLKHY 102
>gnl|CDD|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin
like protein family. The first LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 25.0 bits (55), Expect = 4.0
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 1/49 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C AC K + + + GK +H F C +C T L +++ +G YC
Sbjct: 1 CAACKKPIVG-QVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYC 48
>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin. The
fourth LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 24.3 bits (53), Expect = 5.3
Identities = 15/53 (28%), Positives = 20/53 (37%), Gaps = 1/53 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C +C + I G+ FH F C C L S+ +G YC F
Sbjct: 1 CGSCGLPITG-RCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
>gnl|CDD|226583 COG4098, comFA, Superfamily II DNA/RNA helicase required for DNA
uptake (late competence protein) [DNA replication,
recombination, and repair].
Length = 441
Score = 25.9 bits (57), Expect = 6.1
Identities = 7/24 (29%), Positives = 10/24 (41%)
Query: 60 FRCTQCCTVLRMESYTMNNGHLYC 83
+RC +C + G LYC
Sbjct: 40 YRCNRCGNTHIELFAKLPCGCLYC 63
>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 = 24.4 bits (53), Expect = 6.2
Identities = 14/54 (25%), Positives = 23/54 (42%), Gaps = 1/54 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFK 88
C CNK + + + +H CF C+ C L + +T YC+ +K
Sbjct: 1 CVKCNKPITS-GGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53
>gnl|CDD|188832 cd09448, LIM_CLP36, This family represents the LIM domain of
CLP36. This family represents the LIM domain of CLP36.
CLP36 has also been named as CLIM1, Elfin, or PDLIM1.
CLP36 contains a C-terminal LIM domain and an
N-terminal PDZ domain. CLP36 is highly expressed in
heart and is present in many other tissues including
lung, liver, spleen, and blood. CLP36 has been
implicated in many processes including hypoxia and
regulation of actin stress fibers. CLP36 co-localizes
with alpha-actinin-2 at the Z-lines in myocardium. In
addition, CLP36 binds to alpha-actinin-1 and
alpha-actinin-4, and associates with F-actin filaments
and stress fibers. CLP36 might be involved in not only
the function of sarcomeres in muscle cells, but also in
actin stress fiber-mediated cellular processes, such as
cell shape, migration, polarit, and cytokinesis in
non-muscle cells. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 24.1 bits (52), Expect = 6.7
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 56 HRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
H C+ CT C T L+ + + +YC H
Sbjct: 21 HPECYVCTDCGTNLKQKGHFFVEDQIYCEKH 51
>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 = 24.2 bits (52), Expect = 7.2
Identities = 13/55 (23%), Positives = 24/55 (43%), Gaps = 2/55 (3%)
Query: 35 CFACNKKVYPLEKIE-TDGKLFHRACFRCTQCCTVLRM-ESYTMNNGHLYCLPHF 87
C C + ++ + + G ++H ACF C C L E + + + C H+
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55
>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 = 24.1 bits (52), Expect = 7.7
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 53 KLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
K +H ACF C++C L + + +YC
Sbjct: 24 KHWHEACFLCSKCKISLVDKPFGSKADRIYC 54
>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1. The
first LIM domain of Prickle 1. Prickle contains three
C-terminal LIM domains and a N-terminal PET domain
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in mainly expressed in
fetal brain, adult cartilage, pancreatic islet, and
some types of timorous cells. In addition, Prickle 1
regulates cell movements during gastrulation and
neuronal migration through interaction with the
noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations
in prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 59
Score = 24.1 bits (52), Expect = 8.4
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 52 GKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
G +H +CF C C +L Y +G ++C H
Sbjct: 23 GVCWHPSCFVCFTCNELLVDLIYFYQDGKIHCGRH 57
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 24.1 bits (52), Expect = 9.1
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 1/49 (2%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C +C K + + + G+ +H F C QC L + NG YC
Sbjct: 3 CASCQKPIAG-QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYC 50
>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 = 23.9 bits (52), Expect = 9.4
Identities = 7/13 (53%), Positives = 10/13 (76%)
Query: 53 KLFHRACFRCTQC 65
K++H CFRC+ C
Sbjct: 20 KIYHIECFRCSAC 32
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.323 0.135 0.439
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,662,758
Number of extensions: 441375
Number of successful extensions: 509
Number of sequences better than 10.0: 1
Number of HSP's gapped: 502
Number of HSP's successfully gapped: 168
Length of query: 117
Length of database: 10,937,602
Length adjustment: 80
Effective length of query: 37
Effective length of database: 7,389,282
Effective search space: 273403434
Effective search space used: 273403434
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 (22.0 bits)
S2: 53 (24.1 bits)