RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy327
(168 letters)
>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 = 100 bits (251), Expect = 1e-28
Identities = 35/47 (74%), Positives = 40/47 (85%)
Query: 1 MSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 47
++VFASRAGP +CWHP CF CS C ELLVDLIYFY+ K+YCGRHHA
Sbjct: 13 IAVFASRAGPGACWHPACFVCSTCKELLVDLIYFYQDGKVYCGRHHA 59
>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 = 93.0 bits (232), Expect = 6e-26
Identities = 32/46 (69%), Positives = 38/46 (82%)
Query: 1 MSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
++VFA RAG ++CWHPGCF C CNELLVDLIYFY K+YCGRH+
Sbjct: 13 VAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
>gnl|CDD|188804 cd09420, LIM3_Prickle, The third LIM domain of Prickle. The third
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Two
forms of prickles have been identified; namely prickle 1
and prickle 2. Prickle 1 and prickle 2 are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 87.9 bits (218), Expect = 7e-24
Identities = 32/45 (71%), Positives = 38/45 (84%)
Query: 83 GQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACS 127
GQM+++GQHWHAT+ CFCCA C SLLGRPFLP+ G I+CS ACS
Sbjct: 15 GQMTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYCSRACS 59
>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 = 83.4 bits (206), Expect = 5e-22
Identities = 33/47 (70%), Positives = 39/47 (82%)
Query: 1 MSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 47
++VFASRAG +CWHP CF C+ C ELLVDLIYFY+ K+YCGRHHA
Sbjct: 13 IAVFASRAGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYCGRHHA 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 = 81.1 bits (200), Expect = 4e-21
Identities = 34/47 (72%), Positives = 39/47 (82%)
Query: 1 MSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 47
++VFASRAGP CWHP CF C CNELLVDLIYFY+ K++CGRHHA
Sbjct: 13 VAVFASRAGPGVCWHPSCFVCFTCNELLVDLIYFYQDGKIHCGRHHA 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 = 80.4 bits (198), Expect = 7e-21
Identities = 36/47 (76%), Positives = 40/47 (85%)
Query: 1 MSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 47
++VFASRAG CWHP CF CSVCNELLVDLIYFY+ K+YCGRHHA
Sbjct: 13 IAVFASRAGHGVCWHPQCFVCSVCNELLVDLIYFYQDGKIYCGRHHA 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 = 72.9 bits (179), Expect = 6e-18
Identities = 28/45 (62%), Positives = 35/45 (77%)
Query: 2 SVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
+V+A RAG + WHP CF CS C ELLVD+IYF++ KLYCGRH+
Sbjct: 14 AVYAERAGYDKLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58
>gnl|CDD|188728 cd09342, LIM3_Testin_like, The third LIM domain of Testin-like
family. The third LIM domain of Testin_like family:
This family includes testin, prickle, dyxin and
LIMPETin. Structurally, testin and prickle proteins
contain three LIM domains at C-terminal; LIMPETin has
six LIM domains; and dyxin presents only two LIM
domains. However, all members of the family contain a
PET protein-protein interaction domain. Testin is a
cytoskeleton associated focal adhesion protein that
localizes along actin stress fibers, at
cell-cell-contact areas, and at focal adhesion plaques.
Testin interacts with a variety of cytoskeletal
proteins, including zyxin, mena, VASP, talin, and actin
and it is involved in cell motility and adhesion events.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). Dyxin
involves in lung and heart development by interaction
with GATA6 and blocking GATA6 activated target genes.
LIMPETin might be the recombinant product of genes
coding testin and four and half LIM proteins and its
function is not well understood. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 57
Score = 72.4 bits (178), Expect = 9e-18
Identities = 27/46 (58%), Positives = 34/46 (73%)
Query: 82 AGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACS 127
+++H GQHWHAT+ CFCC+ C SLLG+PFLP+ G IFCS C
Sbjct: 12 VQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFCSPKCK 57
>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 = 63.2 bits (154), Expect = 4e-14
Identities = 23/46 (50%), Positives = 30/46 (65%)
Query: 1 MSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
++V A + G + WHP CF CS C ELLVDL Y D++YC RH+
Sbjct: 13 LAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
>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 = 48.3 bits (115), Expect = 1e-08
Identities = 20/45 (44%), Positives = 30/45 (66%)
Query: 84 QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSK 128
++S+ HWHA CF C+ CS L+G+ F+P G++FCS+ C K
Sbjct: 14 RVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK 58
>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1,
Mec-3. Zinc-binding domain family. Some LIM domains
bind protein partners via tyrosine-containing motifs.
LIM domains are found in many key regulators of
developmental pathways.
Length = 54
Score = 47.0 bits (112), Expect = 5e-08
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
WHP CF C+ C + L +F + KLYC
Sbjct: 20 GKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 37.0 bits (86), Expect = 2e-04
Identities = 14/38 (36%), Positives = 19/38 (50%), Gaps = 2/38 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+ G+ WH CF CATC L G F + G ++C
Sbjct: 16 LRALGKVWHP--ECFKCATCGKPLSGDTFFEKDGKLYC 51
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 46.6 bits (111), Expect = 7e-08
Identities = 15/43 (34%), Positives = 20/43 (46%)
Query: 4 FASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
R WHP CF C+VC + L +F + KLYC +
Sbjct: 12 ELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDY 54
Score = 28.5 bits (64), Expect = 0.34
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
G+ WH CF CA C L F + G ++C
Sbjct: 19 GKVWHP--ECFRCAVCGKPLGPGDFFEKDGKLYC 50
>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 = 45.0 bits (107), Expect = 3e-07
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WHP CF CSVC + L ++ + K YC + +
Sbjct: 18 GKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 33.1 bits (76), Expect = 0.007
Identities = 12/38 (31%), Positives = 17/38 (44%), Gaps = 2/38 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+ G+ WH CF C+ C L G F + G +C
Sbjct: 14 LRALGKKWHP--ECFKCSVCGKPLGGDSFYEKDGKPYC 49
>gnl|CDD|188809 cd09425, LIM4_LIMPETin, The fourth LIM domain of protein LIMPETin.
The fourth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 39.0 bits (91), Expect = 5e-05
Identities = 13/39 (33%), Positives = 23/39 (58%), Gaps = 2/39 (5%)
Query: 84 QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+M ++GQ WH + CFCC C + + F+P+ ++C
Sbjct: 14 KMEYKGQQWH--EKCFCCCECKQPIGTKSFIPKDDDVYC 50
Score = 26.2 bits (58), Expect = 2.2
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCG 43
WH CF C C + + + + D +YC
Sbjct: 22 WHEKCFCCCECKQPIGTKSFIPKDDDVYCV 51
>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 = 39.1 bits (91), Expect = 5e-05
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 44
WH CF CS C LVD + + D++YCG
Sbjct: 26 WHEACFLCSKCKISLVDKPFGSKADRIYCGN 56
Score = 38.7 bits (90), Expect = 6e-05
Identities = 15/39 (38%), Positives = 27/39 (69%), Gaps = 2/39 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
+S++ +HWH ++CF C+ C +SL+ +PF +A I+C
Sbjct: 19 LSYKDKHWH--EACFLCSKCKISLVDKPFGSKADRIYCG 55
>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 = 38.5 bits (90), Expect = 6e-05
Identities = 14/31 (45%), Positives = 18/31 (58%)
Query: 15 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
HP CF C+ C L + YF+ D+LYC H
Sbjct: 21 HPECFVCADCGLNLKNKGYFFIEDELYCETH 51
>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 = 37.8 bits (88), Expect = 1e-04
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
+S E + WH CF C+ CS+SL+G F P I C
Sbjct: 17 VSFEDRQWH--QPCFKCSRCSVSLVGAGFFPDGDQILCR 53
Score = 29.7 bits (67), Expect = 0.12
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 44
WH CF CS C+ LV +F GD++ C
Sbjct: 24 WHQPCFKCSRCSVSLVGAGFFPDGDQILCRD 54
>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 = 37.1 bits (86), Expect = 3e-04
Identities = 18/43 (41%), Positives = 24/43 (55%), Gaps = 2/43 (4%)
Query: 86 SHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSIACSK 128
++EG WH D CF C CSL+L + F+ G I+CS K
Sbjct: 23 NYEGSSWH--DYCFNCKKCSLNLANKRFVFHNGQIYCSDCAKK 63
Score = 26.6 bits (59), Expect = 1.8
Identities = 10/31 (32%), Positives = 16/31 (51%)
Query: 12 SCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
S WH CF C C+ L + + + ++YC
Sbjct: 27 SSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57
>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 = 37.1 bits (86), Expect = 3e-04
Identities = 17/38 (44%), Positives = 23/38 (60%), Gaps = 2/38 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+S E +HWH + CF CA C SL+G+ F+ G I C
Sbjct: 17 ISFEDRHWH--NDCFNCAGCRTSLVGKGFITDGGRILC 52
>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 = 36.8 bits (85), Expect = 3e-04
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WH CF CSVC +LL + Y+ + KLYC +H+
Sbjct: 18 QEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKHY 52
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 36.6 bits (85), Expect = 3e-04
Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 86 SHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
S E + WH CF C CS+SL+G+ FL + I C
Sbjct: 18 SFEERQWH--SDCFNCGKCSVSLVGQGFLTQRDEILCP 53
Score = 28.1 bits (63), Expect = 0.50
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCG 43
WH CF C C+ LV + + D++ C
Sbjct: 24 WHSDCFNCGKCSVSLVGQGFLTQRDEILCP 53
>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog
(ENH) family. The third LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 36.1 bits (83), Expect = 6e-04
Identities = 15/32 (46%), Positives = 18/32 (56%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
WH CF CSVC E L +F + DK C +H
Sbjct: 22 WHDTCFVCSVCCESLEGQTFFSKKDKPLCKKH 53
Score = 28.0 bits (62), Expect = 0.43
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
G WH D+CF C+ C SL G+ F + C
Sbjct: 19 GHTWH--DTCFVCSVCCESLEGQTFFSKKDKPLC 50
>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 = 35.0 bits (81), Expect = 0.001
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 11 NSCWHPGCFTCSVCNELLVDL 31
N+ WHP CF C +CN+ L D+
Sbjct: 17 NNNWHPDCFRCEICNKELADI 37
>gnl|CDD|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM
domains protein (FHL). The first LIM domain of Four and
a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 int eracts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 34.7 bits (80), Expect = 0.002
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
+S++ +HWH CF C C SL+ +PF + + C+
Sbjct: 19 LSYKDRHWHEG--CFKCFKCQRSLVDKPFAAKDEDLLCT 55
Score = 33.2 bits (76), Expect = 0.008
Identities = 12/30 (40%), Positives = 15/30 (50%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCG 43
WH GCF C C LVD + + + L C
Sbjct: 26 WHEGCFKCFKCQRSLVDKPFAAKDEDLLCT 55
>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 = 34.2 bits (79), Expect = 0.003
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
M ++G+ WH + CF C+ C + + F+P+ I+C
Sbjct: 15 MEYKGKFWH--EKCFTCSECKKPIGTKSFIPKDDKIYC 50
Score = 31.5 bits (72), Expect = 0.027
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 12 SCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH CFTCS C + + + + DK+YC
Sbjct: 20 KFWHEKCFTCSECKKPIGTKSFIPKDDKIYC 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 = 33.9 bits (78), Expect = 0.003
Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 12 SCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH C CSVC + L YF R KLYC
Sbjct: 19 RSWHEECLQCSVCQQPLTTSCYF-RDRKLYC 48
>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 = 33.9 bits (78), Expect = 0.004
Identities = 12/35 (34%), Positives = 17/35 (48%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
WH CF C+VC+ L ++ + DK C H
Sbjct: 19 GHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNH 53
Score = 32.8 bits (75), Expect = 0.009
Identities = 13/35 (37%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
G WH D+CF CA C ++L G+ F + C
Sbjct: 19 GHTWH--DTCFVCAVCHVNLEGQTFYSKKDKPLCK 51
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain
Kinase ). The first LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerisation. LIMKs can function in both cytoplasm
and nucleus and are expressed in all tissues. Both
LIMK1 and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. However,
LIMK1 and LIMk2 have different cellular locations.
While LIMK1 localizes mainly at focal adhesions, LIMK2
is found in cytoplasmic punctae, suggesting that they
may have different cellular functions. The LIM domains
of LIMK have been shown to play an important role in
regulating kinase activity and likely also contribute
to LIMK function by acting as sites of
protein-to-protein interactions. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 33.6 bits (77), Expect = 0.004
Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
N WH CF CSVC++ L + YF + KLYC + +
Sbjct: 18 NQDWHCDCFRCSVCSDSLSNW-YFEKDGKLYCRKDY 52
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first LIM domain of Four and a
half LIM domains protein 1 (FHL1): FHL1 is heavily
expressed in skeletal and cardiac muscles. It plays
important roles in muscle growth, differentiation, and
sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. .
Length = 54
Score = 33.6 bits (77), Expect = 0.004
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 82 AGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
+ ++ H+ ++WH ++CF CA C L PF+ + I C
Sbjct: 12 SKELHHKNRYWH--ETCFRCAKCYKPLANEPFVAKDNKILCG 51
Score = 29.0 bits (65), Expect = 0.24
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 44
N WH CF C+ C + L + + + +K+ CG+
Sbjct: 19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILCGK 52
>gnl|CDD|188817 cd09433, LIM4_FHL2, The fourth LIM domain of Four and a half LIM
domains protein 2 (FHL2). The fourth LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 58
Score = 32.7 bits (74), Expect = 0.010
Identities = 18/38 (47%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+S E + WH + CF C CSLSL+GR FL I C
Sbjct: 17 ISFEERQWH--NDCFNCKKCSLSLVGRGFLTERDDILC 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 = 0.015
Identities = 12/34 (35%), Positives = 17/34 (50%)
Query: 13 CWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WHP FTCS C+ L ++ + LYC +
Sbjct: 19 SWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
>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 = 31.8 bits (73), Expect = 0.017
Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 1/33 (3%)
Query: 14 WHPGCFTCSVCNELLVDLIYFY-RGDKLYCGRH 45
WH CF C+ C + Y DK YC +H
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQH 56
>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 = 31.8 bits (72), Expect = 0.018
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
+HP CF C C L YF+ ++LYC H
Sbjct: 20 YHPECFMCDDCGLNLKQRGYFFIDEQLYCETH 51
>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM
domains protein 1 (FHL1). The second LIM domain of
Four and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth,
differentiation, and sarcomere assembly by acting as a
modulator of transcription factors. Defects in FHL1
gene are responsible for a number of Muscular
dystrophy-like muscle disorders. It has been detected
that FHL1 binds to Myosin-binding protein C, regulating
myosin filament formation and sarcomere assembly. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 32.0 bits (73), Expect = 0.019
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 12 SCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
+ WH CFTCS C + + +F +G+ YC H
Sbjct: 20 NVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCH 54
>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 = 31.8 bits (72), Expect = 0.022
Identities = 15/31 (48%), Positives = 17/31 (54%)
Query: 15 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
HP CF CS CN L YF+ +LYC H
Sbjct: 21 HPECFVCSDCNLNLKQKGYFFVEGQLYCEAH 51
>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 = 31.5 bits (72), Expect = 0.029
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 13 CWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
+H CF CS CN+ L Y KLYC H
Sbjct: 20 LFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53
>gnl|CDD|188833 cd09449, LIM_Mystique, The LIM domain of Mystique, a subfamily of
ALP LIM domain proteins. The LIM domain of Mystique, a
subfamily of ALP LIM domain proteins: Mystique is the
most recently identified member of the ALP protein
family. It also interacts with alpha-actinin, as other
ALP proteins do. Mystique promotes cell attachment and
migration and suppresses anchorage-independent growth.
The LIM domain of Mystique is required for the
suppression function. Moreover, Mystique functions as
an ubiquitin E3 ligase acting on STAT proteins to cause
their proteosome mediated degradation. As in all LIM
domains, this domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 31.0 bits (70), Expect = 0.036
Identities = 13/31 (41%), Positives = 21/31 (67%)
Query: 15 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
HPGC+TC+ C L +F+ G+K++C +H
Sbjct: 22 HPGCYTCTDCGLNLKMRGHFWAGEKMFCEKH 52
>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 = 31.1 bits (71), Expect = 0.039
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLY 41
+ WHP CF C C + + + + G+ Y
Sbjct: 18 GAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a. The first
LIM domain of Lmx1a: Lmx1a belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. Human Lmx1a can be found in pancreas,
skeletal muscle, adipose tissue, developing brain,
mammary glands, and pituitary. The functions of Lmx1a
in the developing nervous system were revealed by
studies of mutant mouse. In mouse, mutations in Lmx1a
result in failure of the roof plate to develop. Lmx1a
may act upstream of other roof plate markers such as
MafB, Gdf7, Bmp 6, and Bmp7. Further characterization
of these mice reveals numerous defects including
disorganized cerebellum, hippocampus, and cortex;
altered pigmentation; female sterility; skeletal
defects; and behavioral abnormalities. Within
pancreatic cells, the Lmx1a protein interacts
synergistically with the bHLH transcription factor E47
to activate the insulin gene enhancer/promoter. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 52
Score = 30.9 bits (70), Expect = 0.042
Identities = 15/36 (41%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
+S WH C C+ C E L FYR KLYC +
Sbjct: 18 DSLWHERCLQCASCKEPLETTC-FYRDKKLYCKEDY 52
>gnl|CDD|188741 cd09355, LIM2_Ajuba_like, The second LIM domain of Ajuba-like
proteins. The second LIM domain of Ajuba-like
proteins: Ajuba like LIM protein family includes three
highly homologous proteins Ajuba, Limd1, and WTIP.
Members of the family contain three tandem C-terminal
LIM domains and a proline-rich N-terminal region. This
family of proteins functions as scaffolds,
participating in the assembly of numerous protein
complexes. In the cytoplasm, Ajuba binds Grb2 to
modulate serum-stimulated ERK activation. Ajuba also
recruits the TNF receptor-associated factor 6 (TRAF6)
to p62 and activates PKCKappa activity. Ajuba interacts
with alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 30.8 bits (70), Expect = 0.044
Identities = 11/15 (73%), Positives = 12/15 (80%)
Query: 14 WHPGCFTCSVCNELL 28
+HPGCF C VCNE L
Sbjct: 20 YHPGCFRCCVCNECL 34
>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 = 30.8 bits (70), Expect = 0.044
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WHP F C+ C L +F R + YC
Sbjct: 20 WHPEHFVCAECKTELGTKNFFERDGQPYC 48
Score = 25.0 bits (55), Expect = 6.3
Identities = 14/43 (32%), Positives = 18/43 (41%), Gaps = 3/43 (6%)
Query: 82 AGQMSHE-GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
GQ+ G+ WH F CA C L + F R G +C
Sbjct: 9 VGQVVTALGKTWHPEH--FVCAECKTELGTKNFFERDGQPYCE 49
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 30.8 bits (69), Expect = 0.057
Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
G WH D+CF CA C ++L G+PF + C
Sbjct: 19 GHTWH--DTCFICAVCHVNLEGQPFYSKKDKPLC 50
Score = 28.9 bits (64), Expect = 0.25
Identities = 12/32 (37%), Positives = 18/32 (56%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
WH CF C+VC+ L ++ + DK C +H
Sbjct: 22 WHDTCFICAVCHVNLEGQPFYSKKDKPLCKKH 53
>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin.
The fifth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is
a transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 30.1 bits (68), Expect = 0.067
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
N WH CFTC+ C++ L + R +K YC
Sbjct: 17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
Score = 29.8 bits (67), Expect = 0.10
Identities = 14/42 (33%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 82 AGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
+G ++++ + WH CF C CS SL G+ F R +C+
Sbjct: 10 SGGVTYKNEPWHRE--CFTCTNCSKSLAGQRFTSRDEKPYCA 49
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 62
Score = 30.6 bits (69), Expect = 0.075
Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 2/39 (5%)
Query: 85 MSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
+S++ +HWH +SCF C C SL+ +PF + + C+
Sbjct: 19 LSYKDRHWH--ESCFHCFQCKNSLVDKPFAAKEEHLLCT 55
Score = 26.8 bits (59), Expect = 1.4
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH CF C C LVD + + + L C
Sbjct: 26 WHESCFHCFQCKNSLVDKPFAAKEEHLLC 54
>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 = 30.3 bits (69), Expect = 0.076
Identities = 11/28 (39%), Positives = 14/28 (50%)
Query: 15 HPGCFTCSVCNELLVDLIYFYRGDKLYC 42
H CFTC VC L +F + + YC
Sbjct: 21 HIKCFTCKVCGCDLAQGGFFVKEGEYYC 48
>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 = 29.5 bits (66), Expect = 0.14
Identities = 11/31 (35%), Positives = 18/31 (58%)
Query: 15 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
HP C+ C+ C L +F+ D++YC +H
Sbjct: 21 HPECYVCTDCGTNLKQKGHFFVEDQIYCEKH 51
>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 = 29.5 bits (66), Expect = 0.16
Identities = 17/43 (39%), Positives = 19/43 (44%), Gaps = 3/43 (6%)
Query: 82 AGQMSHE-GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
AGQ+ GQ WH F C C L RPF R G +C
Sbjct: 11 AGQVVTALGQTWHPEH--FVCCQCGKELGSRPFFERNGQAYCE 51
Score = 27.5 bits (61), Expect = 0.82
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WHP F C C + L +F R + YC
Sbjct: 22 WHPEHFVCCQCGKELGSRPFFERNGQAYC 50
>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 = 29.2 bits (66), Expect = 0.16
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
N+ WHP CF C C++ ++ +F YC H
Sbjct: 17 NTQWHPECFVCRECHKPFINGSFFEHEGLPYCETH 51
>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 = 29.3 bits (66), Expect = 0.18
Identities = 22/71 (30%), Positives = 28/71 (39%), Gaps = 20/71 (28%)
Query: 52 PRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSLLGR 111
PRCSACDE+ EG+HWH FCC C L G+
Sbjct: 1 PRCSACDEI------------------IFADECTEAEGRHWHMKH--FCCFECECQLGGQ 40
Query: 112 PFLPRAGVIFC 122
++ R G +C
Sbjct: 41 RYIMREGRPYC 51
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung to a
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to s upport the assembly of multimeric protein
complexes.
Length = 57
Score = 29.2 bits (65), Expect = 0.19
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 84 QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+M ++G WH T CF C C + + F+P+ FC
Sbjct: 14 KMEYKGNSWHET--CFICQRCQQPIGTKSFIPKDNQNFC 50
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their
LIM, nebulin-like, and SH3 domains ,but differ
significantly at their linker regions. Both proteins
are ubiquitously expressed and involved in cytoskeletal
architecture, especially in the organization of focal
adhesions. LASP-1 and LASP-2, are important during
early embryo- and fetogenesis and are highly expressed
in the central nervous system of the adult. However,
only LASP-1 seems to participate significantly in
neuronal differentiation and plays an important
functional role in migration and proliferation of
certain cancer cells while the role of LASP-2 is more
structural. The expression of LASP-1 in breast tumors
is increased significantly. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 53
Score = 28.9 bits (65), Expect = 0.23
Identities = 15/35 (42%), Positives = 19/35 (54%), Gaps = 4/35 (11%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRG-DKL-YCGRHH 46
WH GCF C VC L + Y+G +K YC H+
Sbjct: 21 WHKGCFKCEVCGMTLN--MKNYKGYNKKPYCNAHY 53
>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 = 28.8 bits (65), Expect = 0.23
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 14 WHPGCFTCSVCNELLVDLIYF-YRGDKLYCGRH 45
+H CFTC+ CN+ L +F R +YC H
Sbjct: 26 FHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLH 58
Score = 25.7 bits (57), Expect = 3.3
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 1/27 (3%)
Query: 97 SCFCCATCSLSLL-GRPFLPRAGVIFC 122
+CF CATC+ L G F R G+++C
Sbjct: 29 NCFTCATCNKPLTKGDHFGMRDGLVYC 55
>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also
known as Lim1) and Lhx5. The second LIM domain of Lhx1
(also known as Lim1) and Lhx5. Lhx1 and Lhx5 are
closely related members of LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx1 is required for regulating the vertebrate head
organizer, the nervous system, and female reproductive
tract development. During embryogenesis in the mouse,
Lhx1 is expressed early in mesodermal tissue, then
later during urogenital, kidney, liver, and nervous
system development. In the adult, expression is
restricted to the kidney and brain. A mouse embryos
with Lhx1 gene knockout cannot grow normal anterior
head structures, kidneys, and gonads, but with normally
developed trunk and tail morphology. In the developing
nervous system, Lhx1 is required to direct the
trajectories of motor axons in the limb. Lhx1 null
female mice lack the oviducts and uterus. Lhx5 protein
may play complementary or overlapping roles with Lhx1.
The expression of Lhx5 in the anterior portion of the
mouse neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 56
Score = 28.9 bits (65), Expect = 0.24
Identities = 11/31 (35%), Positives = 16/31 (51%), Gaps = 6/31 (19%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLY 41
+ +H CFTC VC + L G++LY
Sbjct: 19 DKVFHLNCFTCMVCRKQLST------GEELY 43
>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 = 28.6 bits (64), Expect = 0.26
Identities = 15/34 (44%), Positives = 17/34 (50%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 44
+ WHP F CS C EL D + R K YC R
Sbjct: 17 DQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50
>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 = 28.5 bits (64), Expect = 0.27
Identities = 11/30 (36%), Positives = 13/30 (43%), Gaps = 1/30 (3%)
Query: 13 CWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH C C+ C L D F R +YC
Sbjct: 20 TWHAKCLKCNDCGAQLTDKC-FARNGHVYC 48
>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX
protein family. The first LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group are
found in the nucleus and act as transcription factors
or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Is l2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 28.5 bits (64), Expect = 0.30
Identities = 14/41 (34%), Positives = 19/41 (46%), Gaps = 1/41 (2%)
Query: 7 RAGPNSCWHPGCFTCSVCNELLVD-LIYFYRGDKLYCGRHH 46
R P+ WH C C+ C + L + F R K YC R +
Sbjct: 15 RVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55
>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner
(LPP). The first LIM domain of lipoma preferred partner
(LPP): LPP is a member of the zyxin LIM protein family
and contains three LIM zinc-binding domains at the
C-terminal and proline-rich region at the N-terminal.
LPP initially identified as the most frequent
translocation partner of HMGA2 (High Mobility Group A2)
in a subgroup of benign tumors of adipose tissue
(lipomas). It was also shown to be rearranged in a
number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 28.5 bits (64), Expect = 0.31
Identities = 11/26 (42%), Positives = 15/26 (57%)
Query: 97 SCFCCATCSLSLLGRPFLPRAGVIFC 122
SCF C C ++L G+PF G +C
Sbjct: 25 SCFTCHQCQINLQGKPFYALDGKPYC 50
>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma
subfamily with unknown function. The third LIM domain
of an Enigma subfamily with unknown function: The
Enigma LIM domain family is comprised of three
characterized members: Enigma, ENH, and Cypher
(mouse)/ZASP (human). These subfamily members contain a
single PDZ domain at the N-terminus and three LIM
domains at the C-terminus. They serve as adaptor
proteins, where the PDZ domain tethers the protein to
the cytoskeleton and the LIM domains, recruit signaling
proteins to implement corresponding functions. The
members of the enigma family have been implicated in
regulating or organizing cytoskeletal structure, as
well as involving multiple signaling pathways. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 54
Score = 28.7 bits (64), Expect = 0.31
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
N+ +H CF C+ CN L ++ +G + +C H
Sbjct: 19 NNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLH 53
Score = 24.4 bits (53), Expect = 8.3
Identities = 11/34 (32%), Positives = 19/34 (55%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
++H+ CF C C+++L G+ F + G FC
Sbjct: 19 NNNYHSQ--CFNCTRCNVNLEGQSFYAKGGRPFC 50
>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 = 28.5 bits (64), Expect = 0.32
Identities = 8/29 (27%), Positives = 15/29 (51%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
+H CF C+ C + D +++ + YC
Sbjct: 22 YHEQCFVCAQCFQPFPDGLFYEFEGRKYC 50
>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 = 28.6 bits (64), Expect = 0.33
Identities = 13/45 (28%), Positives = 24/45 (53%), Gaps = 2/45 (4%)
Query: 78 SSLPAGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+ +G ++++ Q WH+ CF C++CS L G+ F +C
Sbjct: 6 KPITSGGVTYQDQPWHS--ECFVCSSCSKKLAGQRFTAVEDQYYC 48
Score = 25.5 bits (56), Expect = 4.0
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH CF CS C++ L + D+ YC
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
>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 = 28.5 bits (63), Expect = 0.33
Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKL-YCGRH 45
+H CFTC+ CN++L +F D L YC H
Sbjct: 26 YHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLH 58
>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 = 28.3 bits (64), Expect = 0.34
Identities = 23/75 (30%), Positives = 33/75 (44%), Gaps = 21/75 (28%)
Query: 52 PRCSACDEVRVQVGGHRTRDLNINYFSSLPAGQMSHEGQHWHATDSCFCCATCSLSLLGR 111
PRC+ACDE + G T+ EG++WH FCC C L G+
Sbjct: 1 PRCAACDE--LIFSGEYTQA----------------EGKNWHLKH--FCCFQCDEPLGGQ 40
Query: 112 PFLPRAGVIFCSIAC 126
++ R G +C + C
Sbjct: 41 RYVLREGKPYC-LDC 54
Score = 27.6 bits (62), Expect = 0.80
Identities = 12/29 (41%), Positives = 13/29 (44%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH F C C+E L Y R K YC
Sbjct: 23 WHLKHFCCFQCDEPLGGQRYVLREGKPYC 51
>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 = 28.3 bits (63), Expect = 0.40
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
N+ WHP CF C C V+ +F + YC H+
Sbjct: 17 NTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
>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 = 28.1 bits (63), Expect = 0.41
Identities = 7/15 (46%), Positives = 9/15 (60%)
Query: 14 WHPGCFTCSVCNELL 28
WH CF C C ++L
Sbjct: 21 WHVWCFKCKECGKVL 35
Score = 25.4 bits (56), Expect = 3.5
Identities = 10/34 (29%), Positives = 15/34 (44%), Gaps = 3/34 (8%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+ WH CF C C L G ++ + G +C
Sbjct: 18 DKQWHV--WCFKCKECGKVLTGE-YMGKDGKPYC 48
>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 = 28.1 bits (63), Expect = 0.42
Identities = 9/29 (31%), Positives = 11/29 (37%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH C C C + L + K YC
Sbjct: 21 WHKPCLRCEKCKKTLTPGQHSEHEGKPYC 49
>gnl|CDD|188842 cd09458, LIM3_Enigma, The third LIM domain of Enigma. The third
LIM domain of Enigma: Enigma was initially characterized
in humans as a protein containing three LIM domains at
the C-terminus and a PDZ domain at N-terminus. The
third LIM domain specifically interacts with the insulin
receptor and the second LIM domain interacts with the
receptor tyrosine kinase Ret and the adaptor protein
APS. Thus Enigma is implicated in signal transduction
processes such as mitogenic activity, insulin related
actin organization, and glucose metabolism. Enigma is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 28.1 bits (62), Expect = 0.43
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
G WH D+CF CA C ++L G+ F + C
Sbjct: 19 GFSWH--DTCFVCAICQINLEGKTFYSKKDKPLC 50
Score = 27.7 bits (61), Expect = 0.73
Identities = 11/32 (34%), Positives = 16/32 (50%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
WH CF C++C L ++ + DK C H
Sbjct: 22 WHDTCFVCAICQINLEGKTFYSKKDKPLCKSH 53
>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher
family. The first LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 52
Score = 28.0 bits (62), Expect = 0.52
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 44
WHP FTC C+ L D+ + + +YC
Sbjct: 20 WHPEEFTCHYCHTSLADVSFVEEQNNVYCEN 50
>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 = 27.9 bits (63), Expect = 0.55
Identities = 12/26 (46%), Positives = 15/26 (57%), Gaps = 2/26 (7%)
Query: 2 SVFAS--RAGPNSCWHPGCFTCSVCN 25
SV+A+ WH CFTC+VCN
Sbjct: 7 SVYAAEEVIAAGKSWHKSCFTCAVCN 32
>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 = 27.7 bits (62), Expect = 0.58
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 4/35 (11%)
Query: 14 WHPGCFTCSVCNEL----LVDLIYFYRGDKLYCGR 44
WH CFTCS C+ L D + + ++ C
Sbjct: 20 WHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54
>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b. The first
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 28.0 bits (62), Expect = 0.59
Identities = 13/29 (44%), Positives = 15/29 (51%), Gaps = 1/29 (3%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH C CS C L + F RGD +YC
Sbjct: 24 WHSKCLKCSDCQTQLAEKC-FSRGDSVYC 51
>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein
(LASP)-like proteins. The LIM domain of LIM and SH3
Protein (LASP) like proteins: This family contains two
types of LIM containing proteins; LASP and N-RAP. LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their
LIM, nebulin-like, and SH3 domains, but differ
significantly at their linker regions. Both proteins
are ubiquitously expressed and involved in cytoskeletal
architecture, especially in the organization of focal
adhesions. LASP-1 and LASP-2, are important during
early embryo- and fetogenesis and are highly expressed
in the central nervous system of the adult. However,
only LASP-1 seems to participate significantly in
neuronal differentiation and plays an important
functional role in migration and proliferation of
certain cancer cells while the role of LASP-2 is more
structural. The expression of LASP-1 in breast tumors
is increased significantly. N-RAP is a muscle-specific
protein concentrated at myotendinous junctions in
skeletal muscle and intercalated disks in cardiac
muscle. LIM domain is found at the N-terminus of N-RAP
and the C-terminal of N-RAP contains a region with
multiple of nebulin repeats. N-RAP functions as a
scaffolding protein that organizes alpha-actinin and
actin into symmetrical I-Z-I structures in developing
myofibrils. Nebulin repeat is known as actin binding
domain. The N-RAP is hypothesized to form antiparallel
dimerization via its LIM domain. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 53
Score = 27.6 bits (61), Expect = 0.61
Identities = 13/33 (39%), Positives = 14/33 (42%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WH CF C VC L Y K YC H+
Sbjct: 21 WHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53
>gnl|CDD|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase
domains protein (Ltd-1). The LIM domain of LIM and
transglutaminase domains protein (Ltd-1): This family
includes mouse Ky protein and Caenorhabditis elegans
Ltd-1 protein. The members of this family consists a
N-terminal Lim domain and a C-terminal
transglutaminase domain. The mouse Ky protein has
putative function in muscle development. The mouse with
ky mutant exhibits combined posterior and lateral
curvature of the spine. The Ltd-1 gene in C. elegans is
expressed in developing hypodermal cells from the
twofold stage embryo through adulthood. These data
define the ltd-1 gene as a novel marker for C. elegans
epithelial cell development. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 55
Score = 27.4 bits (61), Expect = 0.90
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 14 WHPGCFTCSVCN-ELLVDLIYFYRGDK-LYCGRH 45
+H GCF C C L + F +GD +YC RH
Sbjct: 21 YHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
The PINCH LIM4 domain recognizes the third SH3 domain of
another adaptor protein, Nck2. This step is an important
component of integrin signaling event. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the assem
bly of multimeric protein complexes.
Length = 54
Score = 27.3 bits (61), Expect = 0.92
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
G+HWH F CA C LG + G+ +C
Sbjct: 19 GKHWHVEH--FVCAKCEKPFLGHRHYEKKGLAYC 50
Score = 25.4 bits (56), Expect = 4.2
Identities = 8/32 (25%), Positives = 14/32 (43%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
WH F C+ C + + ++ + YC H
Sbjct: 22 WHVEHFVCAKCEKPFLGHRHYEKKGLAYCETH 53
>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP. The LIM domain of
N-RAP: N-RAP is a muscle-specific protein concentrated
at myotendinous junctions in skeletal muscle and
intercalated disks in cardiac muscle. LIM domain is
found at the N-terminus of N-RAP and the C-terminal of
N-RAP contains a region with multiple of nebulin
repeats. N-RAP functions as a scaffolding protein that
organizes alpha-actinin and actin into symmetrical
I-Z-I structures in developing myofibrils. Nebulin
repeat is known as actin binding domain. The N-RAP is
hypothesized to form antiparallel dimerization via its
LIM domain. As in other LIM domains, this domain family
is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 27.2 bits (60), Expect = 0.95
Identities = 12/33 (36%), Positives = 15/33 (45%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WH CF C VC +L + K YC H+
Sbjct: 21 WHKACFHCEVCKMMLTVNNFVSHQKKPYCQAHN 53
>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8.
The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as
the pituitary gland and the pancreas. Studies using
mutant mice have revealed roles for Lhx7 and Lhx8 in
the development of cholinergic neurons in the
telencephalon and in basal forebrain development. Mice
lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8
display dramatically reduced number of forebrain
cholinergic neurons. In addition, Lhx7 mutation affects
male and female mice differently, with females
appearing more affected than males. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 56
Score = 27.2 bits (60), Expect = 1.0
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 13 CWHPGCFTCSVCNELLVDLIYFYRGDK-LYC 42
CWH C +CSVC L Y DK ++C
Sbjct: 21 CWHVRCLSCSVCRTSLGRHTSCYIKDKDIFC 51
>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 = 26.7 bits (59), Expect = 1.2
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
N WHP CF CS C + D +F + C H+
Sbjct: 17 NGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHY 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 = 27.0 bits (59), Expect = 1.2
Identities = 15/36 (41%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKL-YCGRH 45
S +H CFTC+ CN+ L +F D L YC H
Sbjct: 23 ESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAH 58
>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 = 26.7 bits (59), Expect = 1.4
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
+H CF C CN+ L Y LYC H
Sbjct: 21 YHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVH 52
>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 = 1.4
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 84 QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
++ +EGQ WH + CF C C + R F+P +C
Sbjct: 17 KLEYEGQTWH--EHCFICHGCEQPIGSRSFIPDKDEHYC 53
>gnl|CDD|188801 cd09417, LIM2_LIMPETin_like, The second LIM domain of protein
LIMPETin and related proteins. The second LIM domain
of protein LIMPETin: LIMPETin contains 6 LIM domains at
the C-terminal and an N-terminal PET domain. Four of
the six LIM domains are highly homologous to the four
and half LIM domain protein family and two of them show
sequence similarity to the LIM domains of the testin
family. Thus, LIMPETin may be the recombinant product
of genes coding testin and FHL proteins. In
Schistosoma mansoni, where LIMPETin was first
identified, LIMPETin is down regulated in sexually
mature adult Schistosoma females compared to sexually
immature adult females and adult male. Its differential
expression indicates that it is a transcription
regulator. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 56
Score = 26.7 bits (59), Expect = 1.4
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
N WH G F C C+E L Y R + YC
Sbjct: 20 NKDWHSGHFCCWQCDESLTGQRYVLRDEHPYC 51
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved
in actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic
acid (LPA)-induced cell migration. TRIP6 can shuttle to
the nucleus to serve as a coactivator of AP-1 and
NF-kappaB transcriptional factors. Moreover, TRIP6 can
form a ternary complex with the NHERF2 PDZ protein and
LPA2 receptor to regulate LPA-induced activation of ERK
and AKT, rendering cells resistant to chemotherapy.
Recent evidence shows that TRIP6 antagonizes
Fas-Induced apoptosis by enhancing the antiapoptotic
effect of LPA in cells. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 53
Score = 26.8 bits (59), Expect = 1.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 14 WHPGCFTCSVCNELL 28
+HP CFTC VC+ L
Sbjct: 20 YHPHCFTCVVCHRSL 34
>gnl|CDD|215630 PLN03201, PLN03201, RAB geranylgeranyl transferase beta-subunit;
Provisional.
Length = 316
Score = 28.5 bits (64), Expect = 1.6
Identities = 16/44 (36%), Positives = 19/44 (43%), Gaps = 1/44 (2%)
Query: 70 RDLNINYFSSLPAGQMSHEGQHWHATDSCFC-CATCSLSLLGRP 112
D +Y + L S G W D+ F CA C LSLL R
Sbjct: 106 ADKVASYVAGLQNEDGSFSGDEWGEIDTRFSYCALCCLSLLKRL 149
>gnl|CDD|223984 COG1056, NadR, Nicotinamide mononucleotide adenylyltransferase
[Coenzyme metabolism].
Length = 172
Score = 28.1 bits (63), Expect = 1.6
Identities = 12/46 (26%), Positives = 20/46 (43%), Gaps = 6/46 (13%)
Query: 40 LYCGR----H--HAETLKPRCSACDEVRVQVGGHRTRDLNINYFSS 79
+Y GR H H +K S DE+ + +G + N F++
Sbjct: 7 VYFGRFQPLHTGHLYVIKRALSKVDELIIVIGSAQESHTLKNPFTA 52
>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 = 26.5 bits (58), Expect = 1.7
Identities = 15/33 (45%), Positives = 20/33 (60%), Gaps = 3/33 (9%)
Query: 90 QHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+HWH+ SC CA C + L R F RAG ++C
Sbjct: 19 RHWHS--SCLKCADCQMQLAERCF-SRAGNVYC 48
>gnl|CDD|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM
domains protein (FHL). The third LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in
tandem and an N-terminal single zinc finger domain with
a consensus sequence equivalent to the C-terminal half
of a LIM domain. LIMPETin is an exception, containing
six LIM domains. FHL1, 2 and 3 are predominantly
expressed in muscle tissues, and FHL5 is highly
expressed in male germ cells. FHL proteins exert their
roles as transcription co-activators or co-repressors
through a wide array of interaction partners. For
example, FHL1 binds to Myosin-binding protein C,
regulating myosin filament formation and sarcomere
assembly. FHL2 has shown to interact with more than 50
different proteins, including receptors, structural
proteins, transcription factors and cofactors, signal
transducers, splicing factors, DNA replication and
repair enzymes, and metabolic enzymes. FHL3 int eracts
with many transcription factors, such as CREB,
BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 26.1 bits (58), Expect = 2.0
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH CF C+ C + L + R + YC
Sbjct: 20 WHKECFVCTGCKKQLAGQRFTSRDEYPYC 48
Score = 25.4 bits (56), Expect = 4.2
Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 2/43 (4%)
Query: 80 LPAGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+ +G +++ Q WH CF C C L G+ F R +C
Sbjct: 8 ITSGGVTYRDQPWHK--ECFVCTGCKKQLAGQRFTSRDEYPYC 48
>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 = 26.2 bits (58), Expect = 2.2
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 11/47 (23%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSAC 57
N W F+CS C+ L FY D +KP C C
Sbjct: 17 NKTWCVDHFSCSFCDTKLTLKSKFYEFD-----------MKPVCKKC 52
>gnl|CDD|239224 cd02894, GGTase-II, Geranylgeranyltransferase type II
(GGTase-II)_like proteins containing the protein
prenyltransferase (PTase) domain, beta subunit (alpha 6
- alpha 6 barrel fold). GGTase-IIs are a subgroup of the
protein prenyltransferase family of lipid-modifying
enzymes. PTases catalyze the carboxyl-terminal
lipidation of Ras, Rab, and several other cellular
signal transduction proteins, facilitating membrane
associations and specific protein-protein interactions.
Prenyltransferases employ a Zn2+ ion to alkylate a thiol
group catalyzing the formation of thioether linkages
between cysteine residues at or near the C-terminus of
protein acceptors and the C1 atom of isoprenoid lipids
(geranylgeranyl (20-carbon) in the case of GGTase-II ).
GGTase-II catalyzes alkylation of both cysteine residues
in Rab proteins containing carboxy-terminal "CC", "CXCX"
or "CXC" motifs. PTases are heterodimeric with both
alpha and beta subunits required for catalytic activity.
In contrast to other prenyltransferases, GGTas-II
requires an escort protein to bring the substrate
protein to the catalytic heterodimer and to escort the
geryanylgeranylated product to the membrane.
Length = 287
Score = 28.0 bits (63), Expect = 2.3
Identities = 12/39 (30%), Positives = 16/39 (41%), Gaps = 1/39 (2%)
Query: 74 INYFSSLPAGQMSHEGQHWHATDSCFC-CATCSLSLLGR 111
+ L S G W D+ F CA L+LLG+
Sbjct: 106 AKFIKGLQNEDGSFSGDKWGEVDTRFSYCAVLCLTLLGK 144
>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 = 25.9 bits (57), Expect = 2.5
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 14 WHPGCFTCSVCNELL 28
WH CF C +CN+LL
Sbjct: 22 WHKMCFKCGMCNKLL 36
>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 = 26.1 bits (57), Expect = 2.6
Identities = 10/33 (30%), Positives = 16/33 (48%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WH CFTC+ C + + ++ YC R +
Sbjct: 20 WHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 25.0 bits (54), Expect = 5.2
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 2/31 (6%)
Query: 92 WHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
WH CF CA C + R F G +C
Sbjct: 20 WHV--HCFTCAACKTPIRNRAFYMEEGAPYC 48
>gnl|CDD|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like
proteins. The first LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate
serum-stimulated ERK activation. Ajuba also recruits
the TNF receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the
formation or stabilization of adheren junctions by
linking adhesive receptors to the actin cytoskeleton.
Although Ajuba is a cytoplasmic protein, it can shuttle
into the nucleus. In nucleus, Ajuba functions as a
corepressor for the zinc finger-protein Snail. It binds
to the SNAG repression domain of Snail through its LIM
region. Arginine methyltransferase-5 (Prmt5), a
protein in the complex, is recruited to Snai l through
an interaction with Ajuba. This ternary complex
functions to repress E-cadherin, a Snail target gene.
In addition, Ajuba contains functional nuclear-receptor
interacting motifs and selectively interacts with
retinoic acid receptors (RARs) and rexinoid receptor
(RXRs) to negatively regulate retinoic acid signaling.
Wtip, the Wt1-interacting protein, was originally
identified as an interaction partner of the Wilms
tumour protein 1 (WT1). Wtip is involved in kidney and
neural crest development. Wtip interacts with the
receptor tyrosine kinase Ror2 and inhibits canonical
Wnt signaling. LIMD1 was reported to inhibit cell
growth and metastases. The inhibition may be mediated
through an interaction with the protein
barrier-to-autointegration (BAF), a component of
SWI/SNF chromatin-remodeling protein; or through the
interaction with retinoblastoma protein (pRB),
resulting in inhibition of E2F-mediated transcription,
and expression of the majority of genes with E2F1-
responsive elements. Recently, Limd1 was shown to
interact with the p62/sequestosome protein and
influence IL-1 and RANKL signaling by facilitating the
assembly of a p62/TRAF6/a-PKC multi-protein complex.
The Limd1-p62 interaction affects both NF-kappaB and
AP-1 activity in epithelial cells and osteoclasts.
Moreover, LIMD1 functions as tumor repressor to block
lung tumor cell line in vitro and in vivo. Recent
studies revealed that LIM proteins Wtip, LIMD1 and
Ajuba interact with components of RNA induced silencing
complexes (RISC) as well as eIF4E and the mRNA m7GTP
cap-protein complex and are required for
microRNA-mediated gene silencing. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 25.9 bits (57), Expect = 2.8
Identities = 10/31 (32%), Positives = 15/31 (48%)
Query: 12 SCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
+ +H CFTC C L ++ K+YC
Sbjct: 20 NLYHTNCFTCCSCGRTLRGKAFYNVNGKVYC 50
Score = 25.9 bits (57), Expect = 3.1
Identities = 9/27 (33%), Positives = 15/27 (55%)
Query: 96 DSCFCCATCSLSLLGRPFLPRAGVIFC 122
+CF C +C +L G+ F G ++C
Sbjct: 24 TNCFTCCSCGRTLRGKAFYNVNGKVYC 50
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM
and RhoGap domain containing protein. The second LIM
domain of Lrg1p, a LIM and RhoGap domain containing
protein: The members of this family contain three
tandem repeats of LIM domains and a Rho-type GTPase
activating protein (RhoGap) domain. Lrg1p is a Rho1
GTPase-activating protein required for efficient cell
fusion in yeast. Lrg1p-GAP domain strongly and
specifically stimulates the GTPase activity of Rho1p, a
regulator of beta (1-3)-glucan synthase in vitro. The
LIM domain is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 25.8 bits (57), Expect = 3.0
Identities = 13/30 (43%), Positives = 17/30 (56%), Gaps = 3/30 (10%)
Query: 19 FTCSVCNELLV--DLIYFYRGDKLYCGRHH 46
FTCSVC + D Y + G K+YC H+
Sbjct: 25 FTCSVCPTVFGPNDSYYEHEG-KIYCHYHY 53
>gnl|CDD|224974 COG2063, FlgH, Flagellar basal body L-ring protein [Cell motility
and secretion].
Length = 230
Score = 27.7 bits (62), Expect = 3.0
Identities = 12/48 (25%), Positives = 19/48 (39%), Gaps = 3/48 (6%)
Query: 119 VIFCSIACSKGEPPTPSDSSGPGLRPQRPRKSSKAAVTAGPEERGESP 166
+ C C+K P +P PG +P + A + G +G S
Sbjct: 13 LAGCGTECAKVPPLSP---IVPGATVAQPPQPGPAPIQPGSIFQGYSL 57
>gnl|CDD|234938 PRK01297, PRK01297, ATP-dependent RNA helicase RhlB; Provisional.
Length = 475
Score = 27.6 bits (61), Expect = 3.4
Identities = 11/37 (29%), Positives = 17/37 (45%)
Query: 130 EPPTPSDSSGPGLRPQRPRKSSKAAVTAGPEERGESP 166
PP+P+ + P + ++KAA A R E P
Sbjct: 20 APPSPAAAPAPPPPAKTAAPATKAAAPAAAAPRAEKP 56
>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 = 25.5 bits (56), Expect = 3.5
Identities = 15/41 (36%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 7 RAGPNSCWHPGCFTCSVC-NELLVDLIYFYRGDKLYCGRHH 46
RA N +H CFTCS C N+L+ + Y L+C
Sbjct: 16 RAQGN-VYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHDR 55
>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 = 26.0 bits (57), Expect = 3.5
Identities = 12/36 (33%), Positives = 18/36 (50%), Gaps = 1/36 (2%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
NS WH CF C C L Y+ + +L+C + +
Sbjct: 39 NSDWHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 25.7 bits (56), Expect = 3.7
Identities = 13/36 (36%), Positives = 18/36 (50%), Gaps = 2/36 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCSI 124
G+ WH T CF CA C SL + G ++C +
Sbjct: 18 GKPWHKT--CFRCAICGKSLESTTVTDKDGELYCKV 51
>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 = 25.5 bits (56), Expect = 3.9
Identities = 11/29 (37%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH C C C L D + RG ++YC
Sbjct: 24 WHSKCLKCVDCQAQLTDKCF-SRGGQVYC 51
>gnl|CDD|218153 pfam04570, DUF581, Protein of unknown function (DUF581). Family
of uncharacterized proteins.
Length = 59
Score = 25.3 bits (56), Expect = 4.1
Identities = 10/24 (41%), Positives = 14/24 (58%), Gaps = 2/24 (8%)
Query: 21 CSVCNELLVDL--IYFYRGDKLYC 42
C +C + L IY YRG+K +C
Sbjct: 20 CFLCKKKLGPGKDIYMYRGEKAFC 43
>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 = 25.1 bits (55), Expect = 4.2
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
+HP FTCS C ++L + +F ++C
Sbjct: 20 YHPEEFTCSQCKKVLDEGGFFEEKGSIFC 48
>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 = 25.5 bits (56), Expect = 4.4
Identities = 7/11 (63%), Positives = 8/11 (72%)
Query: 14 WHPGCFTCSVC 24
+HP CFTC C
Sbjct: 20 YHPPCFTCVTC 30
>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 = 25.4 bits (55), Expect = 4.6
Identities = 11/38 (28%), Positives = 17/38 (44%)
Query: 9 GPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 46
WHP F C+ C E + +F R + YC + +
Sbjct: 16 AMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved
members of this family. Proteins in this group are
found in the nucleus and act as transcription factors
or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Isl-1 is one of
the LHX proteins isolated originally by virtue of its
ability to bind DNA sequences from the 5'-flanking
region of the rat insulin gene in pancreatic
insulin-producing cells. Mice deficient in Isl-1 fail
to form the dorsal exocrine pancreas and islet cells
fail to differentiate. On the other hand, Isl-1 takes
part in the pituitary development by activating the
gonadotropin-releasing hormone receptor gene together
with LHX3 and steroidogenic factor 1. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Same as Isl1, Isl2 may also be able
to bind to the insulin gene enhancer to promote gene
activation. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 25.1 bits (55), Expect = 4.7
Identities = 16/44 (36%), Positives = 20/44 (45%), Gaps = 2/44 (4%)
Query: 4 FASRAGPNSCWHPGCFTCSVCNELLVDLIYF-YRGDKLYCGRHH 46
F RA +H CF CS C+ L+ F R D L+C H
Sbjct: 13 FVMRAR-TKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55
>gnl|CDD|105864 PRK12699, flgH, flagellar basal body L-ring protein; Reviewed.
Length = 246
Score = 26.8 bits (59), Expect = 5.0
Identities = 10/50 (20%), Positives = 13/50 (26%)
Query: 98 CFCCATCSLSLLGRPFLPRAGVIFCSIACSKGEPPTPSDSSGPGLRPQRP 147
C + S GR P V+ + P P RP
Sbjct: 4 CSMVLSFSARRRGRLLGPVLIVMLALVGGCSLPTPAPKVQQPMSARPPDL 53
>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific
protein SF3. The first Lim domain of pollen specific
protein SF3: SF3 is a Lim protein that is found
exclusively in mature plant pollen grains. It contains
two LIM domains. The exact function of SF3 is unknown.
It may be a transcription factor required for the
expression of late pollen genes. It is possible that
SF3 protein is involved in controlling pollen-specific
processes such as male gamete maturation, pollen tube
formation, or even fertilization. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 63
Score = 25.5 bits (56), Expect = 5.1
Identities = 14/37 (37%), Positives = 16/37 (43%), Gaps = 1/37 (2%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL 50
+H CF CS C L Y LYC + H E L
Sbjct: 25 YHKSCFRCSHCKGTLKLSNYSSMEGVLYC-KPHFEQL 60
>gnl|CDD|188751 cd09365, LIM2_LIMK, The second LIM domain of LIMK (LIM domain
Kinase ). The second LIM domain of LIMK (LIM domain
Kinase ): LIMK protein family is comprised of two
members LIMK1 and LIMK2. LIMK contains two LIM domains,
a PDZ domain and a kinase domain. LIMK is involved in
the regulation of actin polymerization and microtubule
disassembly. LIMK influences architecture of the actin
cytoskeleton by regulating the activity of the cofilin
family proteins cofilin1, cofilin2, and destrin. The
mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus and are expressed in all tissues. Both
LIMK1 and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. However,
LIMK1 and LIMk2 have different cellular locations.
While LIMK1 localizes mainly at focal adhesions, LIMK2
is found in cytoplasmic punctae, suggesting that they
may have different cellular functions. The LIM domains
of LIMK have been shown to play an important role in
regulating kinase activity and likely also contribute
to LIMK function by acting as sites of
protein-to-protein interactions. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 25.0 bits (55), Expect = 5.3
Identities = 13/32 (40%), Positives = 16/32 (50%), Gaps = 2/32 (6%)
Query: 14 WHPGCFTCSVCNELLVD--LIYFYRGDKLYCG 43
+HP CF+CS C + D KLYCG
Sbjct: 20 FHPECFSCSSCKAFIGDGDSYALVERSKLYCG 51
>gnl|CDD|177618 PHA03381, PHA03381, tegument protein VP22; Provisional.
Length = 290
Score = 26.9 bits (59), Expect = 5.8
Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 115 PRAGVIFCSIACSKGEPPTPSDSSGPGLRPQRPRKSSKAAVTAGPEERGESPSR 168
+A F ++ + P + SS RP PR S + A PE G P+R
Sbjct: 55 SQAERRFHHYDEARADYPYYTGSSSEDERPADPRPSRRPH--AQPEASGPGPAR 106
>gnl|CDD|236990 PRK11814, PRK11814, cysteine desulfurase activator complex subunit
SufB; Provisional.
Length = 486
Score = 26.7 bits (60), Expect = 5.9
Identities = 9/11 (81%), Positives = 9/11 (81%)
Query: 114 LPRAGVIFCSI 124
L AGVIFCSI
Sbjct: 149 LAEAGVIFCSI 159
>gnl|CDD|214444 MTH00165, ND5, NADH dehydrogenase subunit 5; Provisional.
Length = 573
Score = 27.0 bits (61), Expect = 6.1
Identities = 11/20 (55%), Positives = 13/20 (65%), Gaps = 2/20 (10%)
Query: 95 TDSCFCCATCSLSLLGRPFL 114
T SCF + +LSL G PFL
Sbjct: 338 TSSCFNIS--NLSLCGFPFL 355
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 24.9 bits (54), Expect = 6.3
Identities = 12/40 (30%), Positives = 21/40 (52%), Gaps = 2/40 (5%)
Query: 84 QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFCS 123
++ +E +H+H + CF C C SL PF + + C+
Sbjct: 18 ELYYEDRHYH--EHCFRCFRCDRSLADEPFTCQDEELLCN 55
>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 = 6.8
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 14 WHPGCFTCSVC 24
+HP CF CSVC
Sbjct: 23 YHPKCFVCSVC 33
>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 = 6.8
Identities = 13/34 (38%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 89 GQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
G+ WH +CF CA C SL + G I+C
Sbjct: 18 GKPWH--KNCFRCAKCGKSLESTTLADKDGEIYC 49
Score = 24.8 bits (54), Expect = 7.3
Identities = 10/34 (29%), Positives = 15/34 (44%)
Query: 9 GPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
G WH CF C+ C + L + ++YC
Sbjct: 16 GAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYC 49
>gnl|CDD|183527 PRK12437, PRK12437, prolipoprotein diacylglyceryl transferase;
Reviewed.
Length = 269
Score = 26.5 bits (59), Expect = 7.1
Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 1/32 (3%)
Query: 65 GGHRTRDLNIN-YFSSLPAGQMSHEGQHWHAT 95
G TR + QM +G ++H T
Sbjct: 147 GRPVTRPFLEGLHLPDFIINQMYIDGVYYHPT 178
>gnl|CDD|214359 CHL00085, ycf24, putative ABC transporter.
Length = 485
Score = 26.5 bits (59), Expect = 7.1
Identities = 9/13 (69%), Positives = 11/13 (84%)
Query: 113 FLPRAGVIFCSIA 125
L +AGVIFCSI+
Sbjct: 147 ELAKAGVIFCSIS 159
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at
the N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of
cell adhesion, cell-cell contacts and transiently in
the nucleus. In nucleus, it acts as a coactivator for
the ETS domain transcription factor PEA3. In addition
to PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and
vasodilator- stimulated phosphoprotein (VASP), has a
weak targeting capacity. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 60
Score = 24.8 bits (54), Expect = 7.4
Identities = 9/15 (60%), Positives = 11/15 (73%)
Query: 14 WHPGCFTCSVCNELL 28
+HP CFTC VC + L
Sbjct: 20 YHPQCFTCVVCGKSL 34
>gnl|CDD|188849 cd09465, LIM2_LIMK2, The second LIM domain of LIMK2 (LIM domain
Kinase 2). The second LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein
family, which comprises LIMK1 and LIMK2. LIMK contains
two LIM domains, a PDZ domain, and a kinase domain.
LIMK is involved in the regulation of actin
polymerization and microtubule disassembly. LIMK
influences architecture of the actin cytoskeleton by
regulating the activity of the cofilin family proteins
cofilin1, cofilin2, and destrin. The mechanism of the
activation is to phosphorylates cofilin on serine 3 and
inactivates its actin-severing activity, altering the
rate of actin depolymerisation. LIMK activity is
activated by phosphorylation of a threonine residue
within the activation loop of the kinase by
p21-activated kinases 1 and 4 and by Rho kinase. LIMKs
can function in both cytoplasm and nucleus. Both LIMK1
and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is
expressed in all tissues. While LIMK1 localizes mainly
at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 59
Score = 24.9 bits (54), Expect = 7.5
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 2/35 (5%)
Query: 14 WHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHH 46
+HP CF C C ++ D + LYCG+ H
Sbjct: 25 YHPECFACMSCKVIIEDGDTYALVQHTTLYCGKCH 59
>gnl|CDD|188812 cd09428, LIM2_FHL5, The second LIM domain of Four and a half LIM
domains protein 5 (FHL5). The second LIM domain of Four
and a half LIM domains protein 5 (FHL5): FHL5 is a
tissue-specific coactivator of CREB/CREM family
transcription factors , which are highly expressed in
male germ cells and is required for post-meiotic gene
expression. FHL5 associates with CREM and confers a
powerful transcriptional activation function. Activation
by CREB has known to occur upon phosphorylation at an
essential regulatory site and the subsequent interaction
with the ubiquitous coactivator CREB-binding protein
(CBP). However, the activation by FHL5 is independent of
phosphorylation and CBP association. It represents a new
route for transcriptional activation by CREM and CREB.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 24.4 bits (53), Expect = 8.0
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 84 QMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
++ EG WH ++CF C +C + +P + + +C
Sbjct: 14 KLEFEGNEWH--ETCFVCQSCQQPIGTKPLITKENKNYC 50
>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 = 24.6 bits (53), Expect = 8.3
Identities = 13/44 (29%), Positives = 19/44 (43%), Gaps = 2/44 (4%)
Query: 79 SLPAGQMSHEGQHWHATDSCFCCATCSLSLLGRPFLPRAGVIFC 122
+ G +++ Q WH CF C C L G+ F R +C
Sbjct: 7 PITTGGVTYRDQPWH--KECFVCTGCKKQLSGQRFTSRDDFAYC 48
>gnl|CDD|236683 PRK10410, PRK10410, hypothetical protein; Provisional.
Length = 100
Score = 25.3 bits (56), Expect = 8.5
Identities = 7/21 (33%), Positives = 10/21 (47%)
Query: 39 KLYCGRHHAETLKPRCSACDE 59
+LYC H + C C+E
Sbjct: 18 RLYCKAKHGGEPQKLCPECEE 38
>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The first LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 24.3 bits (53), Expect = 8.9
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 98 CFCCATCSLSLLGRPFLPRAGVIFC 122
CF C TC+ L G+PF +C
Sbjct: 26 CFTCMTCNGKLRGQPFYAVEKKAYC 50
>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 = 8.9
Identities = 12/35 (34%), Positives = 14/35 (40%)
Query: 11 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 45
+H CF CS CN L Y +YC H
Sbjct: 18 QQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPH 52
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx1 is required
for regulating the vertebrate head organizer, the
nervous system, and female reproductive tract
development. During embryogenesis in the mouse, Lhx1 is
expressed early in mesodermal tissue, then later during
urogenital, kidney, liver, and nervous system
development. In the adult, expression is restricted to
the kidney and brain. A mouse embryos with Lhx1 gene
knockout cannot grow normal anterior head structures,
kidneys, and gonads, but with normally developed trunk
and tail morphology. In the developing nervous system,
Lhx1 is required to direct the trajectories of motor
axons in the limb. Lhx1 null female mice lack the
oviducts and uterus. Lhx5 protein may play
complementary or overlapping roles with Lhx1. The
expression of Lhx5 in the anterior portion of the mouse
neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 24.3 bits (53), Expect = 9.3
Identities = 12/29 (41%), Positives = 13/29 (44%), Gaps = 1/29 (3%)
Query: 14 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 42
WH C C C L + F R KLYC
Sbjct: 21 WHAKCVQCCDCKCPLTEKC-FSREGKLYC 48
>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6. The first LIM
domain of Lhx6. Lhx6 is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Lhx6 functions in the brain and nervous system. It is
expressed at high levels in several regions of the
embryonic mouse CNS, including the telencephalon and
hypothalamus, and the first branchial arch. Lhx6 is
proposed to have a role in patterning of the mandible
and maxilla, and in signaling during odontogenesis. In
brain sections, knockdown of Lhx6 gene blocks the
normal migration of neurons to the cortex. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 54
Score = 24.6 bits (53), Expect = 9.5
Identities = 8/14 (57%), Positives = 8/14 (57%)
Query: 11 NSCWHPGCFTCSVC 24
N WH C CSVC
Sbjct: 18 NLIWHVRCLECSVC 31
>gnl|CDD|178608 PLN03046, PLN03046, D-glycerate 3-kinase; Provisional.
Length = 460
Score = 26.4 bits (58), Expect = 9.9
Identities = 24/104 (23%), Positives = 34/104 (32%), Gaps = 19/104 (18%)
Query: 78 SSLPAGQMSHEGQHWHATDSCFCCATC----------SLSLLGRPFLPRAG------VIF 121
SSL + + H HA D CA+ +L RP+ P +
Sbjct: 8 SSLISSNLQHYMNPIHAADYPIPCASAAAFNFNPISNPFNLKRRPYSPSSHKFNDRVAAS 67
Query: 122 CSIACSKGEPPTPSDSSGPGLRPQRPRKSSK---AAVTAGPEER 162
CS S + S PG + +S A TA +R
Sbjct: 68 CSSYPSSKLSSRKTHLSCPGCGCSWIQDNSMVHDYATTAATSKR 111
>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin. The second
LIM domain of Zyxin: Zyxin exhibits three copies of the
LIM domain, an extensive proline-rich domain and a
nuclear export signal. Localized at sites of
cellsubstratum adhesion in fibroblasts, Zyxin interacts
with alpha-actinin, members of the cysteine-rich
protein (CRP) family, proteins that display Src
homology 3 (SH3) domains and Ena/VASP family members.
Zyxin and its partners have been implicated in the
spatial control of actin filament assembly as well as
in pathways important for cell differentiation. In
addition to its functions at focal adhesion plaques,
recent work has shown that zyxin moves from the sites
of cell contacts to the nucleus, where it directly
participates in the regulation of gene expression. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors o r scaffolds to support the
assembly of multimeric protein.
Length = 60
Score = 24.5 bits (53), Expect = 9.9
Identities = 8/11 (72%), Positives = 9/11 (81%)
Query: 14 WHPGCFTCSVC 24
+HP CFTC VC
Sbjct: 20 YHPQCFTCVVC 30
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.322 0.136 0.459
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: 8,116,166
Number of extensions: 681469
Number of successful extensions: 922
Number of sequences better than 10.0: 1
Number of HSP's gapped: 909
Number of HSP's successfully gapped: 230
Length of query: 168
Length of database: 10,937,602
Length adjustment: 90
Effective length of query: 78
Effective length of database: 6,945,742
Effective search space: 541767876
Effective search space used: 541767876
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 55 (25.0 bits)