RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10674
(138 letters)
>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 = 73.8 bits (182), Expect = 1e-18
Identities = 29/50 (58%), Positives = 36/50 (72%), Gaps = 1/50 (2%)
Query: 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRP 130
PRC ACDELIF EYT AE K +H+KHFCC++CD+ L Q Y+ E +P
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLR-EGKP 49
Score = 39.5 bits (93), Expect = 2e-05
Identities = 14/28 (50%), Positives = 21/28 (75%)
Query: 1 YTLAENKTFHVKHFCCYECDKKVQFENY 28
YT AE K +H+KHFCC++CD+ + + Y
Sbjct: 15 YTQAEGKNWHLKHFCCFQCDEPLGGQRY 42
>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 = 63.8 bits (156), Expect = 7e-15
Identities = 22/36 (61%), Positives = 28/36 (77%)
Query: 39 EVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
+ WHP CFVC TC+ELLVDL+YF++ G +YC R Y
Sbjct: 23 DACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
>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 = 61.9 bits (151), Expect = 5e-14
Identities = 24/34 (70%), Positives = 27/34 (79%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 75
WHP CFVCSTC ELLVDL+YF+ G VYC R +A
Sbjct: 26 WHPACFVCSTCKELLVDLIYFYQDGKVYCGRHHA 59
>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 = 58.7 bits (142), Expect = 9e-13
Identities = 27/47 (57%), Positives = 35/47 (74%)
Query: 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTE 127
PRC CDELIF NEYT AEN+ +H+KHFCC++CD L + Y+ V +
Sbjct: 1 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVND 47
Score = 34.4 bits (79), Expect = 0.002
Identities = 15/28 (53%), Positives = 21/28 (75%)
Query: 1 YTLAENKTFHVKHFCCYECDKKVQFENY 28
YT AEN+ +H+KHFCC++CD + E Y
Sbjct: 15 YTQAENQNWHLKHFCCFDCDNILAGEIY 42
>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 = 58.2 bits (141), Expect = 1e-12
Identities = 28/50 (56%), Positives = 37/50 (74%), Gaps = 1/50 (2%)
Query: 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTESRP 130
PRC ACDE+IF +E T AE + +H+KHFCC+EC+ +L Q YI + E RP
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYI-MREGRP 49
Score = 32.0 bits (73), Expect = 0.014
Identities = 11/19 (57%), Positives = 16/19 (84%)
Query: 2 TLAENKTFHVKHFCCYECD 20
T AE + +H+KHFCC+EC+
Sbjct: 16 TEAEGRHWHMKHFCCFECE 34
>gnl|CDD|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3. The
first LIM domain of Prickle 3/LIM domain only 6 (LM06):
Prickle contains three C-terminal LIM domains and a
N-terminal PET domain. Prickles have been implicated
in roles of regulating tissue polarity or planar cell
polarity (PCP). PCP establishment requires the
conserved Frizzled/Dishevelled PCP pathway. Prickle
interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 54.9 bits (132), Expect = 3e-11
Identities = 21/34 (61%), Positives = 27/34 (79%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 75
WHPQCF C++C ELLVDL+YF+ G +YC R +A
Sbjct: 26 WHPQCFQCASCQELLVDLIYFYQDGKIYCGRHHA 59
>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 = 54.2 bits (130), Expect = 4e-11
Identities = 24/36 (66%), Positives = 29/36 (80%)
Query: 40 VLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 75
V WHPQCFVCS C+ELLVDL+YF+ G +YC R +A
Sbjct: 24 VCWHPQCFVCSVCNELLVDLIYFYQDGKIYCGRHHA 59
>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 = 53.0 bits (127), Expect = 2e-10
Identities = 22/36 (61%), Positives = 28/36 (77%)
Query: 40 VLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 75
V WHP CFVC TC+ELLVDL+YF+ G ++C R +A
Sbjct: 24 VCWHPSCFVCFTCNELLVDLIYFYQDGKIHCGRHHA 59
>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 = 52.8 bits (127), Expect = 2e-10
Identities = 23/34 (67%), Positives = 26/34 (76%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
LWHP CFVCSTC ELLVD++YF G +YC R Y
Sbjct: 25 LWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58
>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin.
The first LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 50.5 bits (121), Expect = 1e-09
Identities = 21/35 (60%), Positives = 25/35 (71%)
Query: 40 VLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
+LWHP CF CSTC+ELLVDL Y + +YC R Y
Sbjct: 24 LLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
>gnl|CDD|188801 cd09417, LIM2_LIMPETin_like, The second LIM domain of protein
LIMPETin and related proteins. The second LIM domain of
protein LIMPETin: LIMPETin contains 6 LIM domains at the
C-terminal and an N-terminal PET domain. Four of the six
LIM domains are highly homologous to the four and half
LIM domain protein family and two of them show sequence
similarity to the LIM domains of the testin family.
Thus, LIMPETin may be the recombinant product of genes
coding testin and FHL proteins. In Schistosoma mansoni,
where LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 48.7 bits (116), Expect = 7e-09
Identities = 23/43 (53%), Positives = 28/43 (65%)
Query: 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYI 123
R CDELIF EYT A NK +H HFCC++CD+ L Q Y+
Sbjct: 1 DRSVQCDELIFSGEYTKAMNKDWHSGHFCCWQCDESLTGQRYV 43
Score = 31.0 bits (70), Expect = 0.031
Identities = 13/28 (46%), Positives = 19/28 (67%)
Query: 1 YTLAENKTFHVKHFCCYECDKKVQFENY 28
YT A NK +H HFCC++CD+ + + Y
Sbjct: 15 YTKAMNKDWHSGHFCCWQCDESLTGQRY 42
>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 = 39.2 bits (92), Expect = 2e-05
Identities = 13/40 (32%), Positives = 17/40 (42%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C C + I E A K +H + F C C K L S+
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSF 40
Score = 36.9 bits (86), Expect = 2e-04
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+CF CS C + L ++ G YC + Y
Sbjct: 21 WHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 37.3 bits (87), Expect = 2e-04
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATM 77
L+H QCFVC+ C + D +++ ++G YC D+ +
Sbjct: 21 LYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVL 57
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 36.2 bits (84), Expect = 3e-04
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYATM 77
+WHP+CF C+ C + L +F G +YC DY +
Sbjct: 21 VWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKL 57
Score = 36.2 bits (84), Expect = 3e-04
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 83 CHACDELIFVNEYTL-AENKTFHVKHFCCYECDKELCNQSY 122
C C + I+ E A K +H + F C C K L +
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDF 41
Score = 24.6 bits (54), Expect = 6.8
Identities = 7/18 (38%), Positives = 9/18 (50%)
Query: 4 AENKTFHVKHFCCYECDK 21
A K +H + F C C K
Sbjct: 17 ALGKVWHPECFRCAVCGK 34
>gnl|CDD|223146 COG0068, HypF, Hydrogenase maturation factor [Posttranslational
modification, protein turnover, chaperones].
Length = 750
Score = 37.7 bits (88), Expect = 8e-04
Identities = 22/113 (19%), Positives = 40/113 (35%), Gaps = 27/113 (23%)
Query: 22 KVQFENYTG-KITQSQESEVLWHPQCFVCSTCDELLVDLM-----YFHYKGNVYCL---- 71
++ +T +I +S+ +TC++ L ++ + Y C
Sbjct: 73 EISESGFTDFRIRKSEGKGNKNTQIPPDAATCEDCLEEIFDPNSRRYLYPFIN-CTNCGP 131
Query: 72 -----------RDYATMLDIPRCHACDELIFVNEYTLAENKTFHVKHFCCYEC 113
R+ +M D P C CD+ EY N+ FH + C +C
Sbjct: 132 RFTIIEALPYDRENTSMADFPLCPFCDK-----EYKDPLNRRFHAQPIACPKC 179
Score = 26.6 bits (59), Expect = 5.1
Identities = 8/42 (19%), Positives = 15/42 (35%)
Query: 1 YTLAENKTFHVKHFCCYECDKKVQFENYTGKITQSQESEVLW 42
Y N+ FH + C +C + N+ G+ +
Sbjct: 161 YKDPLNRRFHAQPIACPKCGPHLFLVNHDGEAIAEANEAIRK 202
>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 = 34.7 bits (80), Expect = 0.001
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRD 73
WHP+CF C+TC + L +F G +YC
Sbjct: 23 WHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 34.7 bits (80), Expect = 0.001
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)
Query: 82 RCHACDELIFVNEYTL-AENKTFHVKHFCCYECDKELCNQSYI 123
+C C + I+ E L A K +H + F C C K L ++
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFF 43
Score = 25.8 bits (57), Expect = 2.1
Identities = 7/22 (31%), Positives = 9/22 (40%)
Query: 1 YTLAENKTFHVKHFCCYECDKK 22
A K +H + F C C K
Sbjct: 15 VLRALGKVWHPECFKCATCGKP 36
>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 = 33.5 bits (77), Expect = 0.003
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ FVC+ C L +F G YC +DY
Sbjct: 20 WHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
Score = 30.8 bits (70), Expect = 0.031
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C AC + I V + A KT+H +HF C EC EL +++
Sbjct: 1 CAACKKPI-VGQVVTALGKTWHPEHFVCAECKTELGTKNF 39
>gnl|CDD|188789 cd09405, LIM1_Paxillin, The first LIM domain of paxillin. The
first LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found
at the interface between the plasma membrane and the
actin cytoskeleton. The binding partners of paxillin
are diverse and include protein tyrosine kinases, such
as Src and FAK, structural proteins, such as vinculin
and actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function
sites to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight cons erved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 32.7 bits (74), Expect = 0.007
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ FVC+ C E + +F G YC +DY
Sbjct: 21 WHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
>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 = 32.5 bits (74), Expect = 0.008
Identities = 15/34 (44%), Positives = 19/34 (55%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
LWHP+CFVC C V+ +F + G YC Y
Sbjct: 19 LWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate
serum-stimulated ERK activation. Ajuba also recruits
the TNF receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 32.4 bits (74), Expect = 0.009
Identities = 19/59 (32%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
C +C K V G Q L+H CF C +C L +++ G VYC DY
Sbjct: 1 CVKCGKGV-----YGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin
like protein family. The third LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 32.3 bits (74), Expect = 0.009
Identities = 13/34 (38%), Positives = 20/34 (58%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+CFVC C + ++ +F ++G YC Y
Sbjct: 19 QWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like
family. The first LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 31.9 bits (73), Expect = 0.011
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ F CS C L ++ + KG++YC Y
Sbjct: 20 WHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
Score = 25.4 bits (56), Expect = 3.0
Identities = 9/41 (21%), Positives = 20/41 (48%), Gaps = 1/41 (2%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYI 123
C C+++I + +A +++H + F C C L ++
Sbjct: 1 CAHCNQVI-RGPFLVALGRSWHPEEFTCSHCHCSLAEIGFV 40
>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 = 31.8 bits (72), Expect = 0.014
Identities = 18/48 (37%), Positives = 25/48 (52%), Gaps = 4/48 (8%)
Query: 30 GKITQSQESEVL---WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
G+I S V+ WH CF CS C +LL + Y+ G +YC + Y
Sbjct: 6 GRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTN-WYYEKDGKLYCHKHY 52
>gnl|CDD|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin. The
first LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 31.4 bits (71), Expect = 0.019
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ FVC C + L +F G YC DY
Sbjct: 22 WHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
Score = 26.0 bits (57), Expect = 2.4
Identities = 13/40 (32%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C +C + I + A +T+H +HF C +C KEL ++ +
Sbjct: 3 CASCQKPI-AGQVVTALGQTWHPEHFVCCQCGKELGSRPF 41
>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 = 31.1 bits (70), Expect = 0.022
Identities = 19/59 (32%), Positives = 31/59 (52%), Gaps = 7/59 (11%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
C +C KK+ TG+I + + + WH CF C+ C + + ++ +G YC RDY
Sbjct: 1 CAKCKKKI-----TGEIMHALK--MTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
>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 = 31.0 bits (70), Expect = 0.026
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 43 HPQCFVCSTCDELLVDLMYFHYKGNVYC 70
HP+CFVCS C+ L YF +G +YC
Sbjct: 21 HPECFVCSDCNLNLKQKGYFFVEGQLYC 48
>gnl|CDD|188836 cd09452, LIM1_Enigma, The first LIM domain of Enigma. The first
LIM domain of Enigma: Enigma was initially
characterized in humans as a protein containing three
LIM domains at the C-terminus and a PDZ domain at
N-terminus. The third LIM domain specifically
interacts with the insulin receptor and the second LIM
domain interacts with the receptor tyrosine kinase Ret
and the adaptor protein APS. Thus Enigma is implicated
in signal transduction processes such as mitogenic
activity, insulin related actin organization, and
glucose metabolism. Enigma is expressed in multiple
tissues, such as skeletal muscle, heart, bone and
brain. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 30.9 bits (70), Expect = 0.028
Identities = 12/33 (36%), Positives = 22/33 (66%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
+HP+ F CS C ++L + +F KG+++C + Y
Sbjct: 20 YHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin.
The third LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 31.0 bits (70), Expect = 0.038
Identities = 13/33 (39%), Positives = 16/33 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH CF+CS C LVD + +YC Y
Sbjct: 26 WHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58
>gnl|CDD|232844 TIGR00143, hypF, [NiFe] hydrogenase maturation protein HypF. A
previously described regulatory effect of HypF
mutatation is attributable to loss of activity of a
regulatory hydrogenase. A zinc finger-like region
CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported
the regulatory hypothesis. However, more recent work
(PUBMED:11375153) shows the direct effect is on the
activity of expressed hydrogenases with nickel/iron
centers, rather than on expression [Protein fate,
Protein modification and repair].
Length = 711
Score = 32.8 bits (75), Expect = 0.042
Identities = 17/83 (20%), Positives = 31/83 (37%), Gaps = 24/83 (28%)
Query: 50 STCDELLVDLM-----YFHYK-------GNVYCL-------RDYATMLDIPRCHACDELI 90
+TC + L +++ + Y G + + R+ +M D P C C +
Sbjct: 69 ATCSDCLEEMLDKNDRRYLYPFISCTHCGPRFTIIEALPYDRENTSMADFPLCPDCAK-- 126
Query: 91 FVNEYTLAENKTFHVKHFCCYEC 113
EY ++ FH + C C
Sbjct: 127 ---EYKDPLDRRFHAQPIACPRC 146
>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 = 30.4 bits (69), Expect = 0.045
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH + FVC+ C++ + ++ KG YC Y
Sbjct: 22 WHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 24.2 bits (53), Expect = 9.7
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 81 PRCHACDELIFVNEYTLAENKTFHVKHFCCYECDK 115
P C AC I T A K +HV+HF C +C+K
Sbjct: 1 PICGACRRPIEGRVVT-ALGKHWHVEHFVCAKCEK 34
>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin. The
third LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 30.6 bits (69), Expect = 0.048
Identities = 13/29 (44%), Positives = 16/29 (55%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WHP+CFVCS C + D +F G C
Sbjct: 20 WHPECFVCSDCLKPFTDGSFFELDGRPLC 48
>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 = 30.4 bits (69), Expect = 0.049
Identities = 14/33 (42%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH CF C C ++L Y G YC RDY
Sbjct: 21 WHVWCFKCKECGKVL-TGEYMGKDGKPYCERDY 52
>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin. The
second LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners
PYK2, FAK, PEP and p95PKL. When expressed in human
leukocytic cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 30.2 bits (68), Expect = 0.052
Identities = 15/33 (45%), Positives = 18/33 (54%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ F CS C EL D + G YC RD+
Sbjct: 20 WHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
>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 = 30.1 bits (68), Expect = 0.060
Identities = 21/48 (43%), Positives = 26/48 (54%), Gaps = 4/48 (8%)
Query: 30 GKITQSQESEVL---WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
GKI SQ + L WH CF CS C + L + YF G +YC +DY
Sbjct: 6 GKILDSQYVQALNQDWHCDCFRCSVCSDSLSN-WYFEKDGKLYCRKDY 52
Score = 24.8 bits (54), Expect = 4.7
Identities = 12/40 (30%), Positives = 17/40 (42%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C C I ++Y A N+ +H F C C L N +
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYF 40
>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH. The
second LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated
protein-protein interactions. PINCH comprises an array
of five LIM domains that interact with integrin-linked
kinase (ILK), Nck2 (also called Nckbeta or Grb4) and
other interaction partners. These interactions are
essential for triggering the FA assembly and for
relaying diverse mechanical and biochemical signals
between Cell-extracellular matrix and the actin
cytoskeleton. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 30.0 bits (68), Expect = 0.064
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WHP CF C C++ L D+ + G C
Sbjct: 20 WHPDCFRCEICNKELADIGFVKNAGRALC 48
Score = 24.6 bits (54), Expect = 6.4
Identities = 12/41 (29%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYI 123
C C E + + A N +H F C C+KEL + ++
Sbjct: 1 CGKCGEFV-IGRVIKAMNNNWHPDCFRCEICNKELADIGFV 40
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain
only protein 4). The second LIM domain of LMO4 (LIM
domain only protein 4): LMO4 is a nuclear protein that
plays important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact
with Smad proteins, and associate with the promoter of
the PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential
role for LMO4 as a negative regulator of BRCA1 in
sporadic breast cancer. LMO4 also forms complex to
both ERa (oestrogen receptor alpha), MTA1 (metastasis
tumor antigen 1), and HDACs (histone deacetylases),
implying that LMO4 is also a component of the MTA1
corepressor complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 30.1 bits (68), Expect = 0.069
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHY-KGNVYCLRD 73
+H +CF CSTC LV FHY G+++C D
Sbjct: 22 YHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54
Score = 27.4 bits (61), Expect = 0.65
Identities = 12/36 (33%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 83 CHACDELIFVNEYTL-AENKTFHVKHFCCYECDKEL 117
C AC + I +E + A+ +H+K F C C +L
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQL 36
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 29.6 bits (66), Expect = 0.082
Identities = 13/33 (39%), Positives = 17/33 (51%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ F C C L D+ + + NVYC Y
Sbjct: 20 WHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
>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 = 29.6 bits (67), Expect = 0.083
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 43 HPQCFVCSTCDELLVDLMYFHYKGNVYC 70
HP+CFVC+ C L + YF + +YC
Sbjct: 21 HPECFVCADCGLNLKNKGYFFIEDELYC 48
>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 = 29.1 bits (66), Expect = 0.13
Identities = 7/23 (30%), Positives = 13/23 (56%)
Query: 40 VLWHPQCFVCSTCDELLVDLMYF 62
+WHP+CF C C + + + +
Sbjct: 19 AVWHPECFRCHACRKPIAEHEFS 41
>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 = 0.15
Identities = 12/33 (36%), Positives = 19/33 (57%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH CFVC+ C + + + ++ G YC +DY
Sbjct: 20 WHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain,
and a short consensus C-terminal region. It is the
smallest molecule in the ALP LIM domain containing
protein family. RIL was identified in rat fibroblasts
and in human lymphocytes. The LIM domain interacts with
the AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 28.7 bits (64), Expect = 0.17
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
L+HP+CF+C C L YF +YC
Sbjct: 19 LYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
>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 = 28.4 bits (64), Expect = 0.23
Identities = 9/30 (30%), Positives = 15/30 (50%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCL 71
WH +CF CS C + + + +YC+
Sbjct: 22 WHEKCFTCSECKKPIGTKSFIPKDDKIYCV 51
Score = 24.6 bits (54), Expect = 5.9
Identities = 15/43 (34%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 83 CHACDELIFVNEYTLA-ENKTFHVKHFCCYECDKELCNQSYIP 124
C AC + I + + K +H K F C EC K + +S+IP
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIP 43
>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the
filamin-binding LIM protein-1 (FBLP-1). The second LIM
domain of the filamin-binding LIM protein-1 (FBLP-1):
Fblp-1 contains a proline-rich domain near its N
terminus and two LIM domains at its C terminus. FBLP-1
mRNA was detected in a variety of tissues and cells
including platelets and endothelial cells. FBLP-1 binds
to Filamins. The association between filamin B and
FBLP-1 may play an unknown role in cytoskeletal
function, cell adhesion, and cell motility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 28.2 bits (63), Expect = 0.28
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 42 WHPQCFVCSTCDELLVDLMY-FHYKGNVYCLRDY 74
+HP CF C TC + D + + VYCL DY
Sbjct: 20 YHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
>gnl|CDD|188818 cd09434, LIM4_FHL3, The fourth LIM domain of Four and a half LIM
domains protein 3 (FHL3). The fourth LIM domain of
Four and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 56
Score = 28.2 bits (63), Expect = 0.34
Identities = 11/29 (37%), Positives = 13/29 (44%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CF CS C LV +F + C
Sbjct: 24 WHQPCFKCSRCSVSLVGAGFFPDGDQILC 52
>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the
paxillin like protein family. The second LIM domain of
the paxillin like protein family: This family consists
of paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton.
Paxillin serves as a platform for the recruitment of
numerous regulatory and structural proteins that
together control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression that
are necessary for cell migration and survival. Leupaxin
is a cytoskeleton adaptor protein, which is
preferentially expressed in hematopoietic cells. It
associates with focal adhesion kinases PYK2 and
pp125FAK and identified to be a component of the
osteoclast pososomal signaling complex. Hic-5 controls
cell proliferation, migration and senescence by
functioning as coactivator for steroid receptors such
as androgen receptor, glucocorticoid receptor and
progesterone receptor. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 28.1 bits (63), Expect = 0.34
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ F C+ C + D + G YC DY
Sbjct: 20 WHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 27.0 bits (60), Expect = 0.80
Identities = 9/20 (45%), Positives = 13/20 (65%)
Query: 98 AENKTFHVKHFCCYECDKEL 117
A +KT+H +HF C +C K
Sbjct: 15 ALDKTWHPEHFFCAQCGKPF 34
Score = 26.6 bits (59), Expect = 1.2
Identities = 9/18 (50%), Positives = 13/18 (72%)
Query: 4 AENKTFHVKHFCCYECDK 21
A +KT+H +HF C +C K
Sbjct: 15 ALDKTWHPEHFFCAQCGK 32
>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 = 28.0 bits (63), Expect = 0.36
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 43 HPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
H +CF C C L +F +G YC DY
Sbjct: 21 HIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
>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 = 27.9 bits (62), Expect = 0.40
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH +CFVCS+C + L + + YC+ Y
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the nucleus
to suppress Rac/Cdc42-dependent cyclin D1 expression.
LIMK1 is expressed in all tissues and is localized to
focal adhesions in the cell. LIMK1 can form homodimers
upon binding of HSP90 and is activated by Rho effector
Rho kinase and MAPKAPK2. LIMK1 is important for normal
central nervous system development, and its deletion has
been implicated in the development of the human genetic
disorder Williams syndrome. Moreover, LIMK1 up-regulates
the promoter activity of urokinase type plasminogen
activator and induces its mRNA and protein expression in
breast cancer cells. The LIM domains have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 74
Score = 28.3 bits (63), Expect = 0.43
Identities = 14/44 (31%), Positives = 21/44 (47%)
Query: 79 DIPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
+P C +C + I+ +Y A N +H F C EC L + Y
Sbjct: 18 VLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYY 61
Score = 25.6 bits (56), Expect = 3.8
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH CF C C L Y+ G ++C +DY
Sbjct: 42 WHADCFRCCECGASLSH-WYYEKDGRLFCKKDY 73
>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 = 27.3 bits (61), Expect = 0.64
Identities = 15/35 (42%), Positives = 22/35 (62%), Gaps = 3/35 (8%)
Query: 42 WHPQCFVCSTCDELLVDLMYF--HYKGNVYCLRDY 74
+HP CF C C+E L D + F + N+YC++DY
Sbjct: 20 YHPGCFRCCVCNECL-DGVPFTVDVENNIYCVKDY 53
>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 = 27.2 bits (60), Expect = 0.71
Identities = 11/33 (33%), Positives = 15/33 (45%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WHP+ F C+ C + G YC +DY
Sbjct: 20 WHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first
LIM domain of Lmx1a: Lmx1a belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. Human Lmx1a can be found in pancreas,
skeletal muscle, adipose tissue, developing brain,
mammary glands, and pituitary. The functions of Lmx1a
in the developing nervous system were revealed by
studies of mutant mouse. In mouse, mutations in Lmx1a
result in failure of the roof plate to develop. Lmx1a
may act upstream of other roof plate markers such as
MafB, Gdf7, Bmp 6, and Bmp7. Further characterization
of these mice reveals numerous defects including
disorganized cerebellum, hippocampus, and cortex;
altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within
pancreatic cells, the Lmx1a protein interacts
synergistically with the bHLH transcription factor E47
to activate the insulin gene enhancer/promoter. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 27.0 bits (60), Expect = 0.75
Identities = 13/37 (35%), Positives = 21/37 (56%), Gaps = 1/37 (2%)
Query: 38 SEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
++ LWH +C C++C E L ++ K +YC DY
Sbjct: 17 NDSLWHERCLQCASCKEPLETTCFYRDK-KLYCKEDY 52
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents a
LIM domain subfamily of Eplin-like family. This family
shows highest homology to the LIM domains on Eplin and
XIRP2 protein families. Epithelial Protein Lost in
Neoplasm is a cytoskeleton-associated tumor suppressor
whose expression inversely correlates with cell growth,
motility, invasion and cancer mortality. Xirp2 is
expressed in muscles and is an important effector of the
Ang II signaling pathway in the heart. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 26.9 bits (59), Expect = 0.84
Identities = 13/40 (32%), Positives = 21/40 (52%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C +C + ++ E +A+ FH FCC C+ +L SY
Sbjct: 1 CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSY 40
>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 = 26.8 bits (60), Expect = 0.85
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKEL 117
C C + ++ E +A+ K FH F C C+K L
Sbjct: 1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTL 35
Score = 24.2 bits (53), Expect = 8.5
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
C C K V + + L+H CF CS C++ L Y +G +YC
Sbjct: 1 CAVCGKTVYP------MERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49
>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 = 27.0 bits (60), Expect = 0.89
Identities = 18/55 (32%), Positives = 23/55 (41%), Gaps = 6/55 (10%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
C CDK V + Q V++H CF CS C L Y +G +YC
Sbjct: 5 CKACDKTVYL------VDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYC 53
Score = 24.3 bits (53), Expect = 9.6
Identities = 11/41 (26%), Positives = 20/41 (48%)
Query: 82 RCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
+C ACD+ +++ + A+ +H F C C L +Y
Sbjct: 4 KCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNY 44
>gnl|CDD|233256 TIGR01063, gyrA, DNA gyrase, A subunit. This model describes the
common type II DNA topoisomerase (DNA gyrase). Two
apparently independently arising families, one in the
Proteobacteria and one in Gram-positive lineages, are
both designated toposisomerase IV [DNA metabolism, DNA
replication, recombination, and repair].
Length = 800
Score = 28.8 bits (65), Expect = 0.95
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 8/37 (21%)
Query: 45 QCFVCSTCDELLVDLMYFHYKGNVYCLRDYATMLDIP 81
Q V ST D L++F +G VY L+ Y IP
Sbjct: 539 QLLVASTHD----YLLFFTNRGKVYWLKVY----QIP 567
>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4. The first LIM
domain of Lhx4. Lhx4 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows
significant sequence similarity to LHX3, particularly
to isoforms Lhx3a. In gene regulation experiments, the
LHX4 protein exhibits regulation roles towards
pituitary genes, acting on their promoters/enhancers.
As in other LIM domains, this domain family is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 26.9 bits (59), Expect = 0.96
Identities = 13/33 (39%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH C C+ C L + F GNVYC D+
Sbjct: 21 WHSSCLKCADCQMQLAERC-FSRAGNVYCKEDF 52
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 26.9 bits (59), Expect = 0.99
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH CFVC C + + ++ G YC DY
Sbjct: 20 WHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
>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 = 27.0 bits (60), Expect = 1.1
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C +C +F+ E L E K +H F C C +L S+
Sbjct: 5 CASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSF 44
>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 = 26.5 bits (59), Expect = 1.1
Identities = 15/59 (25%), Positives = 23/59 (38%), Gaps = 6/59 (10%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
C +C K V F + + WH C C C + L + ++G YC + Y
Sbjct: 1 CPKCGKPVYFAEKKTSLGRD------WHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
>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 = 26.7 bits (59), Expect = 1.2
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH CF+C C++ + + K YC+ Y
Sbjct: 25 WHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57
Score = 24.4 bits (53), Expect = 9.1
Identities = 13/44 (29%), Positives = 25/44 (56%), Gaps = 1/44 (2%)
Query: 82 RCHACDELIFVNEYTLA-ENKTFHVKHFCCYECDKELCNQSYIP 124
+C AC + + L E +T+H F C+ C++ + ++S+IP
Sbjct: 3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIP 46
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog
(ENH) family. The third LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 26.5 bits (58), Expect = 1.4
Identities = 13/29 (44%), Positives = 14/29 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CFVCS C E L +F K C
Sbjct: 22 WHDTCFVCSVCCESLEGQTFFSKKDKPLC 50
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first
LIM domain of Lhx3a: Lhx3a is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 56
Score = 26.3 bits (58), Expect = 1.5
Identities = 13/33 (39%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH +C C C L D F G VYC D+
Sbjct: 24 WHSKCLKCVDCQAQLTD-KCFSRGGQVYCKEDF 55
Score = 24.7 bits (54), Expect = 6.2
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 80 IPRCHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
IP+C CD IF ++K +H K C +C +L ++ +
Sbjct: 1 IPKCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCF 43
>gnl|CDD|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog
(ENH) family. The first LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 26.1 bits (57), Expect = 1.5
Identities = 10/29 (34%), Positives = 16/29 (55%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WHP+ F C+ C + + + KG +YC
Sbjct: 20 WHPEEFNCAHCKSSMAYIGFVEEKGALYC 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 = 26.6 bits (59), Expect = 1.5
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CF C C L + + + G +YC
Sbjct: 29 WHDYCFNCKKCSLNLANKRFVFHNGQIYC 57
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Although Lhx2 and Lhx9 are highly homologous, they
seems to play regulatory roles in different organs. In
animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. Lhx9 is expressed in several
regions of the developing mouse brain , the spinal
cord, the pancreas, in limb mesenchyme, and in the
urogenital region. Lhx9 plays critical roles in gonad
development. Homozygous mice lacking functional Lhx9
alleles exhibit numerous urogenital defects, such as
gonadal agenesis, infertility, and undetectable levels
of testosterone and estradiol coupled with high FSH
levels. Lhx9 null mice are phenotypically female, even
those that are genotypically male. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 26.1 bits (58), Expect = 1.6
Identities = 14/34 (41%), Positives = 15/34 (44%), Gaps = 1/34 (2%)
Query: 42 WHPQCFVCSTCDELLVD-LMYFHYKGNVYCLRDY 74
WH C C C L L F GN+YC DY
Sbjct: 21 WHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>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 = 26.2 bits (58), Expect = 1.6
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CFVC+ C L ++ K C
Sbjct: 22 WHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first
LIM domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In mouse, Lmx1b functions in the developing limbs and
eyes, the kidneys, the brain, and in cranial
mesenchyme. The disruption of Lmx1b gene results kidney
and limb defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 25.8 bits (57), Expect = 1.9
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH +C CS C + L YF +YC +DY
Sbjct: 21 WHEECLQCSVCQQPLTTSCYFR-DRKLYCKQDY 52
>gnl|CDD|239454 cd03338, TCP1_delta, TCP-1 (CTT or eukaryotic type II) chaperonin
family, delta subunit. Chaperonins are involved in
productive folding of proteins. They share a common
general morphology, a double toroid of 2 stacked rings.
In contrast to bacterial group I chaperonins (GroEL),
each ring of the eukaryotic cytosolic chaperonin (CTT)
consists of eight different, but homologous subunits.
Their common function is to sequester nonnative proteins
inside their central cavity and promote folding by using
energy derived from ATP hydrolysis. The best studied in
vivo substrates of CTT are actin and tubulin.
Length = 515
Score = 27.6 bits (62), Expect = 2.0
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 14/36 (38%)
Query: 66 GNVYCLRDYATMLD-IPRCHACDELIFVNEYTLAEN 100
YC+R +A L+ IP YTLAEN
Sbjct: 423 VEQYCVRAFADALEVIP-------------YTLAEN 445
>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 = 25.9 bits (57), Expect = 2.0
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 6/55 (10%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
C C K V K+ + + ++H CF C C++ L Y ++GN+YC
Sbjct: 1 CRSCGKPVY------KMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYC 49
Score = 24.7 bits (54), Expect = 5.8
Identities = 12/40 (30%), Positives = 22/40 (55%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C +C + ++ E +AE +H F C +C+K+L +Y
Sbjct: 1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNY 40
>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The third LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 56
Score = 26.1 bits (58), Expect = 2.1
Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 4/33 (12%)
Query: 42 WHPQCFVCSTC----DELLVDLMYFHYKGNVYC 70
WH +CF CS C L D + + + C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILC 52
>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 = 25.9 bits (57), Expect = 2.3
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CF CS C + + +F + YC
Sbjct: 22 WHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50
>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 = 25.8 bits (56), Expect = 2.5
Identities = 12/34 (35%), Positives = 16/34 (47%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 75
WH CF C+ C + L +G +YC YA
Sbjct: 21 WHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54
>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function.
The first Lim domain of a LIM domain containing
protein: The functions of the proteins are unknown. The
members of this family contain two copies of LIM
domain. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 58
Score = 25.7 bits (57), Expect = 2.6
Identities = 11/34 (32%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 42 WHPQCFVCSTCDELLVDLMYFH-YKGNVYCLRDY 74
WH +CFVC+TC + + YC + Y
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>gnl|CDD|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein
(CRP) family. The LIM domains of Cysteine Rich Protein
(CRP) family: Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The known CRP
family members include CRP1, CRP2, and CRP3/MLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription control, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1, CRP2, and CRP3/MLP are involved in
promoting protein assembly along the actin-based
cytoskeleton. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 25.6 bits (57), Expect = 2.7
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKEL 117
C C + ++ E +A K++H F C C+K L
Sbjct: 1 CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRL 35
>gnl|CDD|188816 cd09432, LIM6_LIMPETin, The sixth LIM domain of protein LIMPETin.
The sixth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 25.5 bits (56), Expect = 2.8
Identities = 10/29 (34%), Positives = 13/29 (44%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CF C+ C LV + G + C
Sbjct: 24 WHNDCFNCAGCRTSLVGKGFITDGGRILC 52
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost
in Neoplasm (Eplin) like proteins. The Lim domain of
Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of the
F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising F-actin.
Xirp2 is expressed in muscles and is significantly
induced in the heart in response to systemic
administration of angiotensin II. Xirp2 is an important
effector of the Ang II signaling pathway in the heart.
The expression of Xirp2 is activated by myocyte enhancer
factor (MEF)2A, whose transcriptional activity is
stimulated by angiotersin II. Thus, Xirp2 plays
important pathological roles in the angiotensin II
induced hypertension. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 25.5 bits (56), Expect = 2.8
Identities = 11/40 (27%), Positives = 20/40 (50%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSY 122
C C + ++ E +A+ + FH F C C+ +L +Y
Sbjct: 1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNY 40
>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 = 26.4 bits (58), Expect = 2.9
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 39 EVLWHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
L+H CF C C++ L ++ +G YC
Sbjct: 52 GHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYC 83
>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 = 25.5 bits (56), Expect = 2.9
Identities = 18/59 (30%), Positives = 25/59 (42%), Gaps = 5/59 (8%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
C +C +KV E +G Q ++H CF C C L ++ G YC DY
Sbjct: 1 CVKCGEKVLGEG-SGCTAMDQ----VYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
>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 = 25.8 bits (56), Expect = 3.0
Identities = 13/33 (39%), Positives = 22/33 (66%), Gaps = 1/33 (3%)
Query: 39 EVLWHPQCFVCSTCDELLVDLMYFHYKGN-VYC 70
++++H CF C+TC+++L +F K N VYC
Sbjct: 23 DLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYC 55
>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 = 25.5 bits (56), Expect = 3.0
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH CF C C++LL ++G +YC
Sbjct: 22 WHKMCFKCGMCNKLLDSTNCAEHEGELYC 50
>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 = 25.7 bits (57), Expect = 3.1
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 1/40 (2%)
Query: 80 IPRCHACDELIFVNEYTL-AENKTFHVKHFCCYECDKELC 118
+ RC C I +E + A + FH+ F C C+K L
Sbjct: 2 VKRCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLT 41
Score = 24.5 bits (54), Expect = 6.7
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 39 EVLWHPQCFVCSTCDELLVDLMYFHYK-GNVYCLRDY 74
++++H CF C+TC++ L +F + G VYC Y
Sbjct: 23 DLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
The LHX3 and LHX4 LIM-homeodomain transcription factors
play essential roles in pituitary gland and nervous
system development. Although LHX3 and LHX4 share marked
sequence homology, the genes have different expression
patterns. They play overlapping, but distinct functions
during the establishment of the specialized cells of
the mammalian pituitary gland and the nervous system.
Lhx3 proteins have been demonstrated the ability to
directly bind to the promoters/enhancers of several
pituitary hormone gene promoters to cause increased
transcription. Lhx3a and Lhx3b, whose mRNAs have
distinct temporal expression profiles during
development, are two isoforms of Lhx3. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 52
Score = 25.5 bits (56), Expect = 3.3
Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDY 74
WH +C C+ C L D F G+VYC D+
Sbjct: 21 WHAKCLKCNDCGAQLTD-KCFARNGHVYCKDDF 52
>gnl|CDD|188803 cd09419, LIM3_Testin, The third LIM domain of Testin. The third
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction
domain at the N-terminal. Testin is a cytoskeleton
associated focal adhesion protein that localizes along
actin stress fibers at cell-cell-contact areas and at
focal adhesion plaques. Testin interacts with a variety
of cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility
and adhesion events. Knockout mice experiments reveal
that tumor repressor function of Testin. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 59
Score = 25.2 bits (55), Expect = 3.6
Identities = 12/31 (38%), Positives = 19/31 (61%), Gaps = 2/31 (6%)
Query: 42 WH--PQCFVCSTCDELLVDLMYFHYKGNVYC 70
WH P+CF+CS C + L+ + +G V+C
Sbjct: 22 WHAEPECFLCSCCSKCLIGQKFMPVEGMVFC 52
>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 = 25.4 bits (55), Expect = 3.7
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 39 EVLWHPQCFVCSTCDELLVDLMYFHYKGN-VYC 70
E ++H CF C+TC++ L +F K N VYC
Sbjct: 23 ESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYC 55
>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 = 25.4 bits (55), Expect = 3.8
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 42 WHPQCFVCSTCD-ELLVDLMYFHYKGNVYCLRDY 74
WH +C C C L +L F G++YC DY
Sbjct: 31 WHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 64
>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 = 25.0 bits (55), Expect = 4.1
Identities = 14/36 (38%), Positives = 21/36 (58%), Gaps = 2/36 (5%)
Query: 83 CHACDELIFV-NEYTLAENKTFHVKHFCCYECDKEL 117
C C E I + Y L ++ +H+ F CY+CDK+L
Sbjct: 1 CVGCKESITEGHAYELGGDR-WHIHCFKCYKCDKKL 35
Score = 25.0 bits (55), Expect = 4.6
Identities = 8/16 (50%), Positives = 9/16 (56%)
Query: 41 LWHPQCFVCSTCDELL 56
WH CF C CD+ L
Sbjct: 20 RWHIHCFKCYKCDKKL 35
>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 = 4.2
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 83 CHACDELIFVNEYTL-AENKTFHVKHFCCYECDKEL 117
C C E I +E + A +H++ FCC C+++L
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQL 36
>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 = 24.9 bits (55), Expect = 4.3
Identities = 12/35 (34%), Positives = 16/35 (45%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKEL 117
C+ C + ++V E AE FH F C C L
Sbjct: 1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTL 35
>gnl|CDD|163542 TIGR03830, CxxCG_CxxCG_HTH, putative zinc finger/helix-turn-helix
protein, YgiT family. This model describes a family of
predicted regulatory proteins with a conserved zinc
finger/HTH architecture. The amino-terminal region
contains a novel domain, featuring two CXXC motifs and
occuring in a number of small bacterial proteins as
well as in the present family. The carboxyl-terminal
region consists of a helix-turn-helix domain, modeled
by pfam01381. The predicted function is DNA binding and
transcriptional regulation.
Length = 127
Score = 26.1 bits (58), Expect = 4.5
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 9/47 (19%)
Query: 49 CSTCD--ELLVDL--MYFHYKGNVYCLRDYATMLDIPRCHACDELIF 91
C C EL+ D+ + YKG + C AC E +
Sbjct: 1 CPICGSGELVRDVKDEPYTYKG-----ESITIGVPGWYCPACGEELL 42
>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 = 25.0 bits (55), Expect = 4.8
Identities = 8/11 (72%), Positives = 10/11 (90%)
Query: 42 WHPQCFVCSTC 52
+HP+CFVCS C
Sbjct: 23 YHPKCFVCSVC 33
>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 = 24.9 bits (54), Expect = 5.5
Identities = 10/28 (35%), Positives = 16/28 (57%)
Query: 43 HPQCFVCSTCDELLVDLMYFHYKGNVYC 70
HP+C+VC+ C L +F + +YC
Sbjct: 21 HPECYVCTDCGTNLKQKGHFFVEDQIYC 48
>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 = 24.8 bits (54), Expect = 5.6
Identities = 12/34 (35%), Positives = 15/34 (44%)
Query: 42 WHPQCFVCSTCDELLVDLMYFHYKGNVYCLRDYA 75
WH CF C+ C + L G +YC YA
Sbjct: 21 WHKNCFRCAKCGKSLESTTLADKDGEIYCKGCYA 54
>gnl|CDD|173700 cd05609, STKc_MAST, Catalytic domain of the Protein
Serine/Threonine Kinase, Microtubule-associated
serine/threonine kinase. Serine/Threonine Kinases
(STKs), Microtubule-associated serine/threonine (MAST)
kinase subfamily, MAST, catalytic (c) domain. STKs
catalyze the transfer of the gamma-phosphoryl group from
ATP to serine/threonine residues on protein substrates.
The MAST kinase subfamily is part of a larger
superfamily that includes the catalytic domains of other
protein STKs, protein tyrosine kinases, RIO kinases,
aminoglycoside phosphotransferase, choline kinase, and
phosphoinositide 3-kinase. MAST kinases contain an
N-terminal domain of unknown function, a central
catalytic domain, and a C-terminal PDZ domain that
mediates protein-protein interactions. There are four
mammalian MAST kinases, named MAST1-MAST4. MAST1 is also
referred to as syntrophin-associated STK (SAST), while
MAST2 is also called MAST205. MAST kinases are
cytoskeletal associated kinases of unknown function that
are also expressed at neuromuscular junctions and
postsynaptic densities. MAST1, MAST2, and MAST3 bind and
phosphorylate the tumor suppressor PTEN, and may
contribute to the regulation and stabilization of PTEN.
MAST2 is involved in the regulation of the Fc-gamma
receptor of the innate immune response in macrophages,
and may also be involved in the regulation of the Na+/H+
exchanger NHE3.
Length = 305
Score = 26.3 bits (58), Expect = 5.7
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 96 TLAENKTFHVKHFCCYECDKELC 118
T AEN F V FC +E + LC
Sbjct: 56 TFAENP-FVVSMFCSFETKRHLC 77
>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 = 25.0 bits (54), Expect = 5.9
Identities = 17/56 (30%), Positives = 25/56 (44%), Gaps = 7/56 (12%)
Query: 16 CYECDKKVQFENYTGKITQSQESEVLWHPQCFVCSTCDELLVDLMYFHYKGNVYCL 71
C +C K + TG +T + WH +CFVC+ C + L + YCL
Sbjct: 1 CVQCKKPIT----TGGVTYRDQP---WHKECFVCTGCKKQLSGQRFTSRDDFAYCL 49
>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 = 24.2 bits (53), Expect = 7.6
Identities = 13/34 (38%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 42 WHPQCFVCSTCDELLVD-LMYFHYKGNVYCLRDY 74
WH C C+ C + L + F G YC RDY
Sbjct: 22 WHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>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 = 24.5 bits (53), Expect = 7.7
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 41 LWHPQCFVCSTCDELLVDLMYFHYKGNVYC 70
++H CF CS C+ L Y GN+YC
Sbjct: 20 IYHNSCFRCSYCNTKLSLGTYASLHGNIYC 49
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The first LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 57
Score = 24.6 bits (54), Expect = 7.9
Identities = 11/45 (24%), Positives = 20/45 (44%), Gaps = 2/45 (4%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKELCNQSYIPVTE 127
C C + I ++ A +H+ F C++C K + PV +
Sbjct: 1 CAKCGKPI-TGQFVRALGDVYHLDCFTCHDCGK-PVASKFFPVDD 43
>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH. The
fifth LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 24.2 bits (53), Expect = 8.6
Identities = 14/35 (40%), Positives = 21/35 (60%), Gaps = 1/35 (2%)
Query: 83 CHACDELIFVNEYTLAENKTFHVKHFCCYECDKEL 117
C+ C+++I + A NKT+ V HF C CD +L
Sbjct: 1 CYHCNQVI-EGDVVSALNKTWCVDHFSCSFCDTKL 34
>gnl|CDD|173681 cd05590, STKc_nPKC_eta, Catalytic domain of the Protein
Serine/Threonine Kinase, Novel Protein Kinase C eta.
Serine/Threonine Kinases (STKs), Novel Protein Kinase C
(nPKC), eta isoform, catalytic (c) domain. STKs catalyze
the transfer of the gamma-phosphoryl group from ATP to
serine/threonine residues on protein substrates. The
nPKC subfamily is part of a larger superfamily that
includes the catalytic domains of other protein STKs,
protein tyrosine kinases, RIO kinases, aminoglycoside
phosphotransferase, choline kinase, and phosphoinositide
3-kinase. PKCs are classified into three groups
(classical, atypical, and novel) depending on their mode
of activation and the structural characteristics of
their regulatory domain. nPKCs are calcium-independent,
but require DAG (1,2-diacylglycerol) and
phosphatidylserine (PS) for activity. There are four
nPKC isoforms, delta, epsilon, eta, and theta. PKC-eta
is predominantly expressed in squamous epithelia, where
it plays a crucial role in the signaling of cell-type
specific differentiation. It is also expressed in pro-B
cells and early-stage thymocytes, and acts as a key
regulator in early B-cell development. PKC-eta increases
glioblastoma multiforme (GBM) proliferation and
resistance to radiation, and is being developed as a
therapeutic target for the management of GBM.
Length = 320
Score = 25.6 bits (56), Expect = 8.9
Identities = 18/73 (24%), Positives = 33/73 (45%), Gaps = 8/73 (10%)
Query: 2 TLAENKTFHVKHFCCYECDKKV----QFENYTGKITQSQESEVLWHPQ-CFVCSTCDELL 56
+LA N F + +CC++ ++ +F N + Q+S + F + E+
Sbjct: 50 SLARNHPFLTQLYCCFQTPDRLFFVMEFVNGGDLMFHIQKSRRFDEARARFYAA---EIT 106
Query: 57 VDLMYFHYKGNVY 69
LM+ H KG +Y
Sbjct: 107 SALMFLHDKGIIY 119
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
0.325 0.138 0.471
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,491,141
Number of extensions: 528438
Number of successful extensions: 869
Number of sequences better than 10.0: 1
Number of HSP's gapped: 851
Number of HSP's successfully gapped: 267
Length of query: 138
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 51
Effective length of database: 7,078,804
Effective search space: 361019004
Effective search space used: 361019004
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.7 bits)