RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8131
(198 letters)
>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 = 102 bits (255), Expect = 6e-29
Identities = 44/56 (78%), Positives = 50/56 (89%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCA 193
C +C KPITGIGGT+FISFEDRHWHNDCF CA C++SLVG+GFITDG I+CPDCA
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDCA 56
Score = 39.0 bits (91), Expect = 7e-05
Identities = 14/39 (35%), Positives = 24/39 (61%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
+++++ WH +CF C+ C TSL G+ F + + C DC
Sbjct: 17 ISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55
Score = 35.1 bits (81), Expect = 0.002
Identities = 14/37 (37%), Positives = 19/37 (51%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
++ R WH CF C C+T + K FI I C +C
Sbjct: 19 FEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILCPDC 55
>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 = 93.2 bits (232), Expect = 1e-25
Identities = 33/56 (58%), Positives = 44/56 (78%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCA 193
C +C KPITG+GG +FISFE+R WH+DCF C C SLVG+GF+T ++I+CP+C
Sbjct: 1 CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPECG 56
Score = 42.7 bits (101), Expect = 3e-06
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
++++ WH +CF C CS SL GQ F ++ D+ C +C
Sbjct: 17 ISFEERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55
Score = 35.8 bits (83), Expect = 0.001
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
RQWH CF C C + + F+ + EI C C
Sbjct: 22 RQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55
>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 = 85.6 bits (212), Expect = 1e-22
Identities = 40/47 (85%), Positives = 45/47 (95%)
Query: 84 QIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+II SGGVTYKNEPWHRECFTC+NCS SLAGQRFTSR++KP+CADCF
Sbjct: 6 KIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 38.2 bits (89), Expect = 1e-04
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
YK WH +CF C C + + F R+++ YCA+C+
Sbjct: 15 YKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52
Score = 36.3 bits (84), Expect = 5e-04
Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C K I G +++++ WH +CF C +C SL G+ F + E C DC
Sbjct: 1 CSKCNKIINSGG----VTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADC 51
>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 = 80.8 bits (199), Expect = 1e-20
Identities = 35/57 (61%), Positives = 45/57 (78%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAK 194
C C PI+G+GGT++ISFE+R WHNDCF C C SLVGRGF+T+ +DI+CP+C K
Sbjct: 1 CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPECGK 57
Score = 38.4 bits (89), Expect = 1e-04
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
++++ WH +CF C CS SL G+ F + D C +C
Sbjct: 17 ISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55
Score = 31.9 bits (72), Expect = 0.026
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
+ ++ RQWH CF C C + + F+ +I C C
Sbjct: 17 ISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55
>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 = 79.7 bits (197), Expect = 2e-20
Identities = 30/47 (63%), Positives = 39/47 (82%)
Query: 84 QIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+ ITSGGVTY+++PWH+ECF C+ C LAGQRFTSR++ P+C DCF
Sbjct: 6 KAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
Score = 47.7 bits (114), Expect = 4e-08
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C CKK IT G +++ D+ WH +CF+C C+ L G+ F + E C DC
Sbjct: 1 CAKCKKAITSGG----VTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDC 51
Score = 38.8 bits (91), Expect = 7e-05
Identities = 13/38 (34%), Positives = 23/38 (60%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
Y+ + WH++CF C CK + + F R++ YC +C+
Sbjct: 15 YRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52
>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 = 79.0 bits (195), Expect = 5e-20
Identities = 32/55 (58%), Positives = 39/55 (70%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C +C KPITG GG +++SFEDR WH CF C+ C SLVG GF DG+ I+C DC
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55
Score = 40.9 bits (96), Expect = 1e-05
Identities = 17/39 (43%), Positives = 23/39 (58%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
V++++ WH+ CF CS CS SL G F D+ C DC
Sbjct: 17 VSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55
Score = 37.0 bits (86), Expect = 3e-04
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
++ RQWH+ CF C C + F P +I C +C
Sbjct: 19 FEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQILCRDC 55
>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 = 72.1 bits (177), Expect = 3e-17
Identities = 27/40 (67%), Positives = 32/40 (80%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
MEYK +QWHEKCF C CK PIGTKSFIP++ ++YC CY
Sbjct: 15 MEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54
Score = 37.8 bits (88), Expect = 2e-04
Identities = 12/38 (31%), Positives = 20/38 (52%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
YK + WH +CF C C + + F ++D +C C+
Sbjct: 17 YKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54
Score = 33.2 bits (76), Expect = 0.008
Identities = 12/43 (27%), Positives = 22/43 (51%)
Query: 150 GTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
G + + ++ + WH CF C C+ + + FI +D+ C C
Sbjct: 11 GMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPC 53
>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 = 67.5 bits (165), Expect = 1e-15
Identities = 30/45 (66%), Positives = 38/45 (84%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
ITSGGVTY+++PWH ECF CS+CS LAGQRFT+ ED+ +C DC+
Sbjct: 8 ITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52
Score = 46.0 bits (109), Expect = 2e-07
Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAK 194
C C KPIT G ++++D+ WH++CF+C+SC L G+ F + C DC K
Sbjct: 1 CVKCNKPITSGG----VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53
Score = 39.4 bits (92), Expect = 4e-05
Identities = 13/39 (33%), Positives = 21/39 (53%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
Y+ + WH +CF C C + + F E + YC +CY+
Sbjct: 15 YQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53
>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 = 65.0 bits (158), Expect = 1e-14
Identities = 29/50 (58%), Positives = 40/50 (80%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFA 135
IT+GGVTY+++PWH+ECF C+ C L+GQRFTSR+D +C +CF L+A
Sbjct: 8 ITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
Score = 39.6 bits (92), Expect = 5e-05
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C CKKPIT G +++ D+ WH +CF+C C+ L G+ F + + C +C
Sbjct: 1 CVQCKKPITTGG----VTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNC 51
Score = 36.9 bits (85), Expect = 4e-04
Identities = 15/43 (34%), Positives = 24/43 (55%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFA 45
Y+ + WH++CF C CK + + F R+ YC NC+ +A
Sbjct: 15 YRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
>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 = 61.3 bits (149), Expect = 4e-13
Identities = 26/61 (42%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 135 AKRCYSCKKPITGIG-GTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCA 193
AK+C C+ PITG G GT +++E WH+ CF C C +L + F+ I C DCA
Sbjct: 2 AKKCSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDCA 61
Query: 194 K 194
K
Sbjct: 62 K 62
Score = 41.7 bits (98), Expect = 7e-06
Identities = 16/39 (41%), Positives = 22/39 (56%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
V Y+ WH CF C CS +LA +RF + +C+DC
Sbjct: 22 VNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
Score = 33.6 bits (77), Expect = 0.006
Identities = 13/37 (35%), Positives = 20/37 (54%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
Y+ WH+ CF C C + K F+ +IYC++C
Sbjct: 24 YEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
>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 = 60.4 bits (147), Expect = 6e-13
Identities = 27/40 (67%), Positives = 31/40 (77%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
MEYK + WHEKCF C CK PIGTKSFIP++ +IYC CY
Sbjct: 15 MEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
Score = 41.1 bits (97), Expect = 1e-05
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C +C K I G++ + ++ + WH CF C+ C+ + + FI + I C C
Sbjct: 1 CKACGKAIMP--GSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPC 53
Score = 36.5 bits (85), Expect = 5e-04
Identities = 17/50 (34%), Positives = 27/50 (54%), Gaps = 2/50 (4%)
Query: 83 FQIITSGG--VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+ I G + YK + WH +CFTCS C + + F ++DK +C C+
Sbjct: 5 GKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
>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 = 57.1 bits (138), Expect = 1e-11
Identities = 24/43 (55%), Positives = 30/43 (69%)
Query: 2 EYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKF 44
EYK WH+ CF C CK PIGTKSF P+ ++ YC C+E+KF
Sbjct: 16 EYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
Score = 39.4 bits (92), Expect = 5e-05
Identities = 19/59 (32%), Positives = 29/59 (49%), Gaps = 2/59 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAKAK 196
C C K I G + + ++ WH DCF C++C+ + + F GED C C + K
Sbjct: 1 CKGCYKDILA--GDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKK 57
Score = 39.4 bits (92), Expect = 5e-05
Identities = 18/54 (33%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 83 FQIITSGG--VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELF 134
++ I +G V YK WH++CFTCSNC + + F + + +C C + F
Sbjct: 5 YKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of
Four and a half LIM domains protein 2 (FHL2): FHL2 is
one of the best studied FHL proteins. FHL2 expression
is most abundant in the heart, and in brain, liver and
lung to a lesser extent. FHL2 participates in a wide
range of cellular processes, such as transcriptional
regulation, signal transduction, and cell survival by
binding to various protein partners. FHL2 has shown to
interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. Although FHL2 is abundantly
expressed in heart, the fhl2 null mice are viable and
had no detectable abnormal cardiac phenotype. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to s
upport the assembly of multimeric protein complexes.
Length = 57
Score = 54.3 bits (130), Expect = 1e-10
Identities = 24/43 (55%), Positives = 31/43 (72%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEK 43
MEYK WHE CF C C+ PIGTKSFIP++ + +C CYE++
Sbjct: 15 MEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCYEKQ 57
Score = 34.6 bits (79), Expect = 0.002
Identities = 19/55 (34%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C CKK I + GTR + ++ WH CF+C CQ + + FI C C
Sbjct: 1 CSECKKTI--MPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPC 53
Score = 34.3 bits (78), Expect = 0.004
Identities = 12/38 (31%), Positives = 19/38 (50%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
YK WH CF C C + + F ++++ FC C+
Sbjct: 17 YKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPCY 54
>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 = 53.6 bits (129), Expect = 3e-10
Identities = 26/59 (44%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 134 FAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
FA C CKK I ++ +S++DRHWH CF C CQ SLV + F ED++C +C
Sbjct: 1 FANTCEECKKKIGC--DSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTEC 57
Score = 43.2 bits (102), Expect = 2e-06
Identities = 15/38 (39%), Positives = 22/38 (57%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
YK R WHE CF C C+ + K F +++++ C CY
Sbjct: 21 YKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
Score = 41.7 bits (98), Expect = 9e-06
Identities = 14/45 (31%), Positives = 24/45 (53%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
S ++YK+ WH CF C C SL + F ++++ C +C+
Sbjct: 14 CDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58
>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 = 52.2 bits (125), Expect = 1e-09
Identities = 22/41 (53%), Positives = 29/41 (70%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
+EY+ + WHE CF C C+ PIG++SFIP + E YC CYE
Sbjct: 18 LEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCYE 58
Score = 40.6 bits (95), Expect = 2e-05
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
+C +C K T + G+R + +E + WH CF+C C+ + R FI D ++ C C
Sbjct: 3 KCVACGK--TVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPC 56
Score = 32.9 bits (75), Expect = 0.013
Identities = 11/38 (28%), Positives = 19/38 (50%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
Y+ + WH CF C C + + F +D+ +C C+
Sbjct: 20 YEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57
>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 = 51.8 bits (124), Expect = 2e-09
Identities = 23/59 (38%), Positives = 35/59 (59%), Gaps = 2/59 (3%)
Query: 134 FAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
++ C CKKPI + +S++DRHWH CF C C++SLV + F E ++C +C
Sbjct: 1 YSNTCEECKKPIGC--DCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTEC 57
Score = 40.7 bits (95), Expect = 2e-05
Identities = 17/44 (38%), Positives = 24/44 (54%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKF 44
+ YK R WHE CF C CK + K F +E+ + C CY ++
Sbjct: 19 LSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSNEY 62
Score = 38.3 bits (89), Expect = 1e-04
Identities = 14/40 (35%), Positives = 23/40 (57%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
++YK+ WH CF C C SL + F ++E+ C +C+
Sbjct: 19 LSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECY 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 = 49.7 bits (119), Expect = 8e-09
Identities = 20/56 (35%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 137 RCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
+C C KPI G R + + WH +CF CA+C L G F + C DC
Sbjct: 1 KCAGCGKPIYG--TERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 43.9 bits (104), Expect = 1e-06
Identities = 14/39 (35%), Positives = 21/39 (53%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
+ + WH ECF C+ C L+G F ++ K +C DC
Sbjct: 16 LRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 39.7 bits (93), Expect = 3e-05
Identities = 11/39 (28%), Positives = 21/39 (53%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
+ + WH +CF C C P+ +F ++ ++YC +C
Sbjct: 16 LRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
>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 = 48.3 bits (115), Expect = 3e-08
Identities = 24/59 (40%), Positives = 38/59 (64%), Gaps = 2/59 (3%)
Query: 134 FAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
FA +C C K I GI ++ +S++D+HWH CF+C+ C+ SLV + F + + I C +C
Sbjct: 1 FANQCEECSKII-GID-SKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNC 57
Score = 43.3 bits (102), Expect = 2e-06
Identities = 18/45 (40%), Positives = 28/45 (62%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
I S ++YK++ WH CF CS C SL + F S+ D+ +C +C+
Sbjct: 14 IDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58
Score = 41.8 bits (98), Expect = 7e-06
Identities = 18/41 (43%), Positives = 23/41 (56%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
+ YK + WHE CF C CK + K F + IYC NCY+
Sbjct: 19 LSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCYD 59
>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 = 44.6 bits (106), Expect = 5e-07
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+ + WH ECF CS C L G F ++ KP+C C+
Sbjct: 14 LRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 43.8 bits (104), Expect = 1e-06
Identities = 15/40 (37%), Positives = 23/40 (57%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ ++WH +CF C VC P+G SF ++ + YC CY
Sbjct: 14 LRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 43.5 bits (103), Expect = 1e-06
Identities = 17/56 (30%), Positives = 21/56 (37%), Gaps = 3/56 (5%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCA 193
C C KPI G + + WH +CF C+ C L G F C C
Sbjct: 1 CAGCGKPIEG---RELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 24.6 bits (54), Expect = 9.0
Identities = 14/62 (22%), Positives = 25/62 (40%), Gaps = 9/62 (14%)
Query: 105 CSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRHWHND 164
C+ C + G+ K + +CF +C C KP +GG F + + +
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECF------KCSVCGKP---LGGDSFYEKDGKPYCEK 51
Query: 165 CF 166
C+
Sbjct: 52 CY 53
>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 = 44.1 bits (104), Expect = 9e-07
Identities = 18/40 (45%), Positives = 26/40 (65%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+E++ +WHE CF C C+ PIGTK I +E + YC C+
Sbjct: 15 LEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPCF 54
Score = 36.0 bits (83), Expect = 9e-04
Identities = 21/55 (38%), Positives = 28/55 (50%), Gaps = 2/55 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C+ CKK I + G+R + FE WH CF+C SCQ + + IT C C
Sbjct: 1 CFHCKKTI--MPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPC 53
Score = 32.9 bits (75), Expect = 0.010
Identities = 11/38 (28%), Positives = 20/38 (52%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
++ WH CF C +C + + ++E+K +C CF
Sbjct: 17 FEGNEWHETCFVCQSCQQPIGTKPLITKENKNYCVPCF 54
>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin. The first LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cell substratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 87
Score = 44.5 bits (105), Expect = 1e-06
Identities = 16/33 (48%), Positives = 21/33 (63%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+H CFTC C L GQ+F S E KP+C +C+
Sbjct: 55 FHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
Score = 27.1 bits (60), Expect = 2.3
Identities = 10/35 (28%), Positives = 15/35 (42%)
Query: 158 DRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
+H CF C C+ L G+ F + C +C
Sbjct: 52 GHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEEC 86
Score = 25.6 bits (56), Expect = 7.9
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+H CF C C+ + + F E + YC CY
Sbjct: 53 HLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
>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 = 42.4 bits (100), Expect = 3e-06
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCA 193
C C+KPI ++ + ++R+WH CF CA C L F+ I+C C
Sbjct: 1 CAECRKPIGA--DSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKCT 54
Score = 40.9 bits (96), Expect = 1e-05
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
+ +KN WH CF C+ C LA + F ++++K C C
Sbjct: 15 LHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53
Score = 38.2 bits (89), Expect = 1e-04
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANC 39
+K R WHE CF C C P+ + F+ ++ +I C C
Sbjct: 17 HKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53
>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 = 42.2 bits (100), Expect = 4e-06
Identities = 16/33 (48%), Positives = 20/33 (60%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH + F C C L GQR+ RE KP+C DC+
Sbjct: 23 WHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55
Score = 37.2 bits (87), Expect = 3e-04
Identities = 15/36 (41%), Positives = 22/36 (61%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
+ WH K F C C P+G + ++ RE + YC +CYE
Sbjct: 21 KNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
Score = 34.1 bits (79), Expect = 0.004
Identities = 11/36 (30%), Positives = 16/36 (44%)
Query: 157 EDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
E ++WH F C C L G+ ++ C DC
Sbjct: 19 EGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDC 54
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 41.9 bits (99), Expect = 5e-06
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 94 KNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELF 134
+ WH ECF C+ C L F ++ K +C + +LF
Sbjct: 18 LGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 40.4 bits (95), Expect = 2e-05
Identities = 14/37 (37%), Positives = 22/37 (59%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKF 44
WH +CF C VC P+G F ++ ++YC + Y + F
Sbjct: 22 WHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 35.0 bits (81), Expect = 0.002
Identities = 15/55 (27%), Positives = 18/55 (32%), Gaps = 2/55 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C KPI + WH +CF CA C L F + C
Sbjct: 1 CAGCGKPIYDRE--LVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHD 53
>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 = 40.4 bits (95), Expect = 2e-05
Identities = 15/35 (42%), Positives = 21/35 (60%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH + F C CKT +GTK+F R+ + YC Y
Sbjct: 18 KTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
Score = 37.3 bits (87), Expect = 3e-04
Identities = 14/40 (35%), Positives = 21/40 (52%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
VT + WH E F C+ C T L + F R+ +P+C +
Sbjct: 13 VTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52
Score = 34.2 bits (79), Expect = 0.003
Identities = 15/43 (34%), Positives = 25/43 (58%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
C +CKKPI G + ++ + WH + F+CA C++ L + F
Sbjct: 1 CAACKKPIVG----QVVTALGKTWHPEHFVCAECKTELGTKNF 39
>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 = 39.9 bits (93), Expect = 3e-05
Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 2/59 (3%)
Query: 134 FAKRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
FA C CK+ I +R + +EDRH+H CF C C SL F E+++C DC
Sbjct: 1 FANTCDECKELIGH--DSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDC 57
Score = 35.7 bits (82), Expect = 0.001
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
Y++ +H CF C C SLA + FT ++++ C DC+
Sbjct: 21 YEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58
Score = 32.6 bits (74), Expect = 0.014
Identities = 13/38 (34%), Positives = 22/38 (57%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
Y+ R +HE CF C C + + F +++E+ C +CY
Sbjct: 21 YEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58
>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 = 39.6 bits (92), Expect = 4e-05
Identities = 17/29 (58%), Positives = 19/29 (65%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF CS C SL GQ F S++DKP C
Sbjct: 22 WHDTCFVCSVCCESLEGQTFFSKKDKPLC 50
Score = 36.9 bits (85), Expect = 5e-04
Identities = 18/52 (34%), Positives = 28/52 (53%), Gaps = 2/52 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C+ C+ PI G RF+ WH+ CF+C+ C SL G+ F + + +C
Sbjct: 1 CHGCEFPIEA--GDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLC 50
Score = 26.9 bits (59), Expect = 1.6
Identities = 9/29 (31%), Positives = 16/29 (55%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYC 36
WH+ CF C VC + ++F ++ + C
Sbjct: 22 WHDTCFVCSVCCESLEGQTFFSKKDKPLC 50
>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 = 38.5 bits (90), Expect = 1e-04
Identities = 16/41 (39%), Positives = 24/41 (58%)
Query: 90 GVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
G T ++ +H +CFTC C+ L GQ F + E K +C C+
Sbjct: 14 GCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 28.1 bits (63), Expect = 0.55
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+H CF C+ C + + F E++ YC CY
Sbjct: 22 FHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like
family. The third LIM domain of Enigma-like family: The
Enigma LIM domain family is comprised of three members:
Enigma, ENH, and Cypher (mouse)/ZASP (human). These
subfamily members contain a single PDZ domain at the
N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone, and brain. The third LIM domain
specifically interacts with the insulin receptor and the
second LIM domain interacts with the receptor tyrosine
kinase Ret and the adaptor protein APS. Thus Enigma is
implicated in signal transduction processes, such as
mitogenic activity, insulin related actin organization,
and glucose metabolism. The second member, ENH protein,
was first identified in rat brain. It has been shown
that ENH interacts with protein kinase D1 (PKD1) via its
LIM domains and forms a complex with PKD1 and the
alpha1C subunit of cardiac L-type voltage-gated calcium
channel in rat neonatal cardiomyocytes. The N-terminal
PDZ domain interacts with alpha-actinin at the Z-line.
ZASP/Cypher is required for maintenance of Z-line
structure during muscle contraction, but not required
for Z-line assembly. In heart, Cypher/ZASP plays a
structural role through its interaction with
cytoskeletal Z-line proteins. In addition, there is
increasing evidence that Cypher/ZASP also performs
signaling functions. Studies reveal that Cypher/ZASP
interacts with and directs PKC to the Z-line, where PKC
phosphorylates downstream signaling targets. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 38.2 bits (89), Expect = 1e-04
Identities = 15/32 (46%), Positives = 19/32 (59%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF C+ C +L GQ F S++DKP C
Sbjct: 19 GHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 35.1 bits (81), Expect = 0.002
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C+ C PI G RF+ WH+ CF+CA C +L G+ F + + +C
Sbjct: 1 CHGCDFPIEA--GDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 28.9 bits (65), Expect = 0.24
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 7 QWHEKCFACVVCKTPIGTKSFIPREQEIYCAN 38
WH+ CF C VC + ++F ++ + C N
Sbjct: 21 TWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKN 52
>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 = 38.3 bits (89), Expect = 1e-04
Identities = 15/36 (41%), Positives = 21/36 (58%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
N+ WH F C C SL GQR+ R++ P+C C+
Sbjct: 20 NKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCY 55
Score = 27.5 bits (61), Expect = 0.82
Identities = 11/36 (30%), Positives = 18/36 (50%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
+ WH F C C + + ++ R++ YC CYE
Sbjct: 21 KDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKCYE 56
Score = 26.0 bits (57), Expect = 3.1
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 158 DRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
++ WH+ F C C SL G+ ++ E C C
Sbjct: 20 NKDWHSGHFCCWQCDESLTGQRYVLRDEHPYCIKC 54
>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 = 37.8 bits (88), Expect = 2e-04
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 2/38 (5%)
Query: 91 VTYKNEPWH--RECFTCSNCSTSLAGQRFTSREDKPFC 126
V + + WH ECF CSNC SL GQ F + + FC
Sbjct: 15 VAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
Score = 34.7 bits (80), Expect = 0.002
Identities = 21/59 (35%), Positives = 33/59 (55%), Gaps = 5/59 (8%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWH--NDCFMCASCQSSLVGRGFITDGEDIIC-PDCA 193
C +C +PI G R ++ +HWH +CF C++C+ SL+G+ F+ I C P C
Sbjct: 1 CDACGEPI-GPDVQR-VAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFCSPKCK 57
Score = 33.9 bits (78), Expect = 0.005
Identities = 12/38 (31%), Positives = 22/38 (57%), Gaps = 2/38 (5%)
Query: 1 MEYKTRQWH--EKCFACVVCKTPIGTKSFIPREQEIYC 36
+ + + WH E+CF C CK + + F+P+ +I+C
Sbjct: 15 VAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
>gnl|CDD|188844 cd09460, LIM3_ZASP_Cypher, The third LIM domain of ZASP/Cypher
family. The third LIM domain of ZASP/Cypher family:
ZASP was identified in human heart and skeletal muscle
and Cypher is a mice ortholog of ZASP. ZASP/Cyppher
contains three LIM domains at the C-terminus and a PDZ
domain at N-terminus. ZASP/Cypher is required for
maintenance of Z-line structure during muscle
contraction, but not required for Z-line assembly. In
heart, Cypher/ZASP plays a structural role through its
interaction with cytoskeletal Z-line proteins. In
addition, there is increasing evidence that Cypher/ZASP
also performs signaling functions. Studies reveal that
Cypher/ZASP interacts with and directs PKC to the
Z-line, where PKC phosphorylates downstream signaling
targets. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 37.3 bits (86), Expect = 3e-04
Identities = 15/29 (51%), Positives = 19/29 (65%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF C+ C +L GQ F S++DKP C
Sbjct: 22 WHDTCFICAVCHVNLEGQPFYSKKDKPLC 50
Score = 35.8 bits (82), Expect = 0.001
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C+ C P+ G +FI WH+ CF+CA C +L G+ F + + +C
Sbjct: 1 CHGCDFPVEA--GDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLC 50
Score = 25.4 bits (55), Expect = 5.2
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYC 36
WH+ CF C VC + + F ++ + C
Sbjct: 22 WHDTCFICAVCHVNLEGQPFYSKKDKPLC 50
>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 = 37.0 bits (86), Expect = 3e-04
Identities = 15/33 (45%), Positives = 19/33 (57%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH + F C C L GQR+ RE +P+C CF
Sbjct: 23 WHMKHFCCFECECQLGGQRYIMREGRPYCCHCF 55
Score = 35.9 bits (83), Expect = 0.001
Identities = 16/40 (40%), Positives = 23/40 (57%)
Query: 2 EYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
E + R WH K F C C+ +G + +I RE YC +C+E
Sbjct: 17 EAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCFE 56
Score = 25.1 bits (55), Expect = 6.4
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 157 EDRHWHNDCFMCASCQSSLVGRGFI 181
E RHWH F C C+ L G+ +I
Sbjct: 19 EGRHWHMKHFCCFECECQLGGQRYI 43
>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 = 36.6 bits (85), Expect = 4e-04
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C + I G F+ R WH + F C+ C SL GF+ + + C C
Sbjct: 1 CAHCNQVIRG----PFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51
Score = 35.0 bits (81), Expect = 0.002
Identities = 14/33 (42%), Positives = 18/33 (54%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH E FTCS+C SLA F + +C C+
Sbjct: 20 WHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
Score = 30.0 bits (68), Expect = 0.10
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R WH + F C C + F+ + +YC CY
Sbjct: 18 RSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 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 = 36.5 bits (85), Expect = 6e-04
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 3/49 (6%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGED 186
C CK I G RF+S WH +CF C +C+ + F G D
Sbjct: 1 CAGCKSEI---GHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGND 46
Score = 29.9 bits (68), Expect = 0.11
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH ECF C C +A F+ + P+ C+
Sbjct: 21 WHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
Score = 26.4 bits (59), Expect = 1.9
Identities = 12/33 (36%), Positives = 16/33 (48%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH +CF C C+ PI F + Y +CY
Sbjct: 21 WHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53
Score = 24.9 bits (55), Expect = 6.7
Identities = 13/43 (30%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 105 CSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITG 147
C+ C + + RF S + +CF RC++C+KPI
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECF------RCHACRKPIAE 37
>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 = 36.0 bits (83), Expect = 0.001
Identities = 19/39 (48%), Positives = 22/39 (56%), Gaps = 2/39 (5%)
Query: 91 VTYKNEPWH--RECFTCSNCSTSLAGQRFTSREDKPFCA 127
V+Y N WH ECF CS CS L GQ+F E FC+
Sbjct: 15 VSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFCS 53
Score = 29.1 bits (65), Expect = 0.26
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 4/54 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWH--NDCFMCASCQSSLVGRGFITDGEDIIC 189
C C I + +S+ + HWH +CF+C+ C L+G+ F+ + C
Sbjct: 1 CQGCHNAIDP--EVQRVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFC 52
>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 = 35.9 bits (83), Expect = 0.001
Identities = 16/39 (41%), Positives = 24/39 (61%), Gaps = 2/39 (5%)
Query: 1 MEYKTRQWH--EKCFACVVCKTPIGTKSFIPREQEIYCA 37
M Y + WH EKCF C CK + + F+P++ +IYC+
Sbjct: 17 MTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYCS 55
Score = 34.0 bits (78), Expect = 0.004
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWH--NDCFMCASCQSSLVGRGFITDGEDIIC 189
C +C + I G+ + ++++ +HWH CF CA C+ SL+GR F+ I C
Sbjct: 3 CDTCGEHI-GVDQGQ-MTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYC 54
Score = 31.3 bits (71), Expect = 0.049
Identities = 14/44 (31%), Positives = 25/44 (56%), Gaps = 2/44 (4%)
Query: 86 ITSGGVTYKNEPWH--RECFTCSNCSTSLAGQRFTSREDKPFCA 127
+ G +TY + WH +CF C+ C SL G+ F ++ + +C+
Sbjct: 12 VDQGQMTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYCS 55
>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 = 35.3 bits (81), Expect = 0.001
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R WH + F C C T + SF+ + +YC NCY
Sbjct: 18 RSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
Score = 31.9 bits (72), Expect = 0.026
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH E FTC C TSLA F ++ +C +C+
Sbjct: 20 WHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
Score = 28.0 bits (62), Expect = 0.50
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 159 RHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
R WH + F C C +SL F+ + ++ C +C
Sbjct: 18 RSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENC 51
>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 = 35.0 bits (81), Expect = 0.001
Identities = 14/34 (41%), Positives = 15/34 (44%)
Query: 7 QWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
QWH +CF C C P SF E YC Y
Sbjct: 19 QWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52
Score = 34.2 bits (79), Expect = 0.004
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
C C KPI +IS + WH +CF+C C + F
Sbjct: 1 CGGCNKPILE----NYISALNTQWHPECFVCRECHKPFINGSF 39
Score = 32.7 bits (75), Expect = 0.011
Identities = 13/41 (31%), Positives = 16/41 (39%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
I ++ N WH ECF C C F E P+C
Sbjct: 8 ILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYC 48
>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 = 34.9 bits (81), Expect = 0.002
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 5 TRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH+ CF C VC + + + + EIYC +CY
Sbjct: 18 GKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSCY 53
Score = 31.4 bits (72), Expect = 0.029
Identities = 10/35 (28%), Positives = 17/35 (48%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
+ WH+ CFTC+ C+ L + + +C C
Sbjct: 18 GKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCKSC 52
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 35.1 bits (81), Expect = 0.002
Identities = 15/33 (45%), Positives = 16/33 (48%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH CF C CK PIG F + E YC Y
Sbjct: 20 WHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 29.4 bits (66), Expect = 0.16
Identities = 16/49 (32%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF-ITDGE 185
C C K I G + + WH CF+CA+C+ + F + DGE
Sbjct: 1 CARCHKKILG----EVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGE 45
Score = 28.2 bits (63), Expect = 0.46
Identities = 9/29 (31%), Positives = 14/29 (48%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF C+ C + F + +P+C
Sbjct: 20 WHVSCFVCAACKQPIGNSLFHMEDGEPYC 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 = 34.7 bits (80), Expect = 0.002
Identities = 16/36 (44%), Positives = 21/36 (58%), Gaps = 1/36 (2%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQ-EIYCANCY 40
+ +H CF CV C IG +SF EQ E+YC + Y
Sbjct: 18 KGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
Score = 25.1 bits (55), Expect = 7.2
Identities = 10/34 (29%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSRE-DKPFCADCF 130
+H CFTC C + + F E ++ +C D +
Sbjct: 20 YHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
>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 = 34.6 bits (79), Expect = 0.003
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF C+ C +L G+ F S++DKP C
Sbjct: 22 WHDTCFVCAICQINLEGKTFYSKKDKPLC 50
Score = 32.7 bits (74), Expect = 0.011
Identities = 18/52 (34%), Positives = 27/52 (51%), Gaps = 2/52 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C+ C I G RF+ WH+ CF+CA CQ +L G+ F + + +C
Sbjct: 1 CHGCDFKIDA--GDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLC 50
Score = 26.9 bits (59), Expect = 1.6
Identities = 9/29 (31%), Positives = 17/29 (58%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYC 36
WH+ CF C +C+ + K+F ++ + C
Sbjct: 22 WHDTCFVCAICQINLEGKTFYSKKDKPLC 50
>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 = 34.6 bits (80), Expect = 0.003
Identities = 14/41 (34%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 3 YKTRQWHEKCFACVVCKTPIGTKS----FIPREQEIYCANC 39
++ ++WH KCF C C I ++ F ++Q I C+NC
Sbjct: 15 FEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
Score = 31.5 bits (72), Expect = 0.035
Identities = 21/60 (35%), Positives = 27/60 (45%), Gaps = 8/60 (13%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQ----SSLVGRGFITDGEDIICPDCA 193
C SC K I I FED+ WH CF C+ C S L F + I+C +C+
Sbjct: 1 CASCGKSIE----DECIKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNCS 56
Score = 31.1 bits (71), Expect = 0.048
Identities = 11/41 (26%), Positives = 25/41 (60%), Gaps = 4/41 (9%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQ----RFTSREDKPFCADC 129
++++ WH +CFTCS C ++ + F +++ + C++C
Sbjct: 15 FEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
>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 = 34.6 bits (79), Expect = 0.003
Identities = 15/33 (45%), Positives = 17/33 (51%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH CF C CKTPI ++F E YC Y
Sbjct: 20 WHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 31.9 bits (72), Expect = 0.022
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CFTC+ C T + + F E P+C
Sbjct: 20 WHVHCFTCAACKTPIRNRAFYMEEGAPYC 48
Score = 27.7 bits (61), Expect = 0.74
Identities = 16/43 (37%), Positives = 21/43 (48%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
C CKK ITG + WH CF CA+C++ + R F
Sbjct: 1 CAKCKKKITG----EIMHALKMTWHVHCFTCAACKTPIRNRAF 39
>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 = 34.2 bits (79), Expect = 0.003
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH+ C C C +L + + E KP+C C+
Sbjct: 21 WHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 33.1 bits (76), Expect = 0.007
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R WH+ C C CK + E + YC CY
Sbjct: 19 RDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 25.4 bits (56), Expect = 5.6
Identities = 13/55 (23%), Positives = 17/55 (30%), Gaps = 3/55 (5%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C KP+ + R WH C C C+ +L C C
Sbjct: 1 CPKCGKPVYFAEKKTSLG---RDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKC 52
>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM
(abLIM) proteins. The first LIM domain of actin binding
LIM (abLIM) proteins: Three homologous members of the
abLIM protein family have been identified; abLIM-1,
abLIM-2 and abLIM-3. The N-terminal of abLIM consists of
four tandem repeats of LIM domains and the C-terminal of
acting binding LIM protein is a villin headpiece domain,
which has strong actin binding activity. The abLIM-1,
which is expressed in retina, brain, and muscle tissue,
has been indicated to function as a tumor suppressor.
AbLIM-2 and -3, mainly expressed in muscle and neuronal
tissue, bind to F-actin strongly. They may serve as a
scaffold for signaling modules of the actin cytoskeleton
and thereby modulate transcription. It has shown that
LIM domains of abLIMs interact with STARS (striated
muscle activator of Rho signaling), which directly binds
actin and stimulates serum-response factor
(SRF)-dependent transcription. All LIM domains are 50-60
amino acids in size and share two characteristic highly
conserved zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 34.2 bits (79), Expect = 0.004
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 4/54 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPD 191
CY C K G + +D+++H CF C C L GF + C D
Sbjct: 1 CYKCGKKCKG----EVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTD 50
Score = 27.6 bits (62), Expect = 0.71
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 9 HEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
H KCF C VC + F +E E YC + Y
Sbjct: 21 HIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
Score = 24.5 bits (54), Expect = 9.7
Identities = 12/30 (40%), Positives = 16/30 (53%)
Query: 99 HRECFTCSNCSTSLAGQRFTSREDKPFCAD 128
H +CFTC C LA F +E + +C D
Sbjct: 21 HIKCFTCKVCGCDLAQGGFFVKEGEYYCTD 50
>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 = 34.1 bits (78), Expect = 0.004
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEI-YCANCYEEKFATR 47
+ +H +CF CVVCK P+ +SFI + +C N Y ++A R
Sbjct: 18 KSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60
Score = 33.4 bits (76), Expect = 0.009
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 4/46 (8%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITD 183
C C + IT R + + +H CF C C+ L G FI D
Sbjct: 1 CAVCDQKIT----DRMLKATGKSYHPQCFTCVVCKCPLEGESFIVD 42
Score = 29.1 bits (65), Expect = 0.29
Identities = 16/55 (29%), Positives = 25/55 (45%), Gaps = 1/55 (1%)
Query: 84 QIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDK-PFCADCFGELFAKR 137
Q IT + + +H +CFTC C L G+ F + P C + + +A R
Sbjct: 6 QKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60
>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 = 33.8 bits (78), Expect = 0.004
Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 1/33 (3%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH CF C C L G+ + ++ KP+C +
Sbjct: 21 WHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52
Score = 26.5 bits (59), Expect = 1.7
Identities = 13/40 (32%), Positives = 17/40 (42%), Gaps = 3/40 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVG 177
C C + I G ++ D+ WH CF C C L G
Sbjct: 1 CAGCGQEIKN--GQALLAL-DKQWHVWCFKCKECGKVLTG 37
Score = 26.1 bits (58), Expect = 2.7
Identities = 11/35 (31%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+QWH CF C C + T ++ ++ + YC Y
Sbjct: 19 KQWHVWCFKCKECGKVL-TGEYMGKDGKPYCERDY 52
>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein
2 (CRP2). The second LIM domain of Cysteine Rich
Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP), which
is a striated muscle-specific factor that enhances
myogenic differentiation. The second LIM domain of
CRP3/MLP interacts with cytoskeletal protein
beta-spectrin. CRP3/MLP also interacts with the basic
helix-loop-helix myogenic transcription factors MyoD,
myogenin, and MRF4 thereby increasing their affinity for
specific DNA regulatory elements. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 33.9 bits (77), Expect = 0.004
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 96 EPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFG 131
+PWH+ CF C+ C SL T +E + +C C+
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54
Score = 32.4 bits (73), Expect = 0.017
Identities = 13/35 (37%), Positives = 19/35 (54%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH+ CF C C + + + +E EIYC CY
Sbjct: 19 KPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
Score = 25.8 bits (56), Expect = 3.6
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 161 WHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
WH +CF CA C SL +I C C
Sbjct: 21 WHKNCFRCAKCGKSLESTTLTEKEGEIYCKGC 52
>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase
). The first LIM domain of LIMK (LIM domain Kinase ):
LIMK protein family is comprised of two members LIMK1
and LIMK2. LIMK contains two LIM domains, a PDZ domain
and a kinase domain. LIMK is involved in the regulation
of actin polymerization and microtubule disassembly.
LIMK influences architecture of the actin cytoskeleton
by regulating the activity of the cofilin family
proteins cofilin1, cofilin2, and destrin. The mechanism
of the activation is to phosphorylates cofilin on serine
3 and inactivates its actin-severing activity, and
altering the rate of actin depolymerisation. LIMKs can
function in both cytoplasm and nucleus and are expressed
in all tissues. Both LIMK1 and LIMK2 can act in the
nucleus to suppress Rac/Cdc42-dependent cyclin D1
expression. However, LIMK1 and LIMk2 have different
cellular locations. While LIMK1 localizes mainly at
focal adhesions, LIMK2 is found in cytoplasmic punctae,
suggesting that they may have different cellular
functions. The LIM domains of LIMK have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 53
Score = 33.6 bits (77), Expect = 0.005
Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFCAD 128
N+ WH +CF CS CS SL+ F ++ K +C
Sbjct: 18 NQDWHCDCFRCSVCSDSLSNWYF-EKDGKLYCRK 50
Score = 28.6 bits (64), Expect = 0.36
Identities = 12/26 (46%), Positives = 14/26 (53%)
Query: 159 RHWHNDCFMCASCQSSLVGRGFITDG 184
+ WH DCF C+ C SL F DG
Sbjct: 19 QDWHCDCFRCSVCSDSLSNWYFEKDG 44
Score = 25.5 bits (56), Expect = 4.5
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 1/35 (2%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH CF C VC + + + ++ ++YC Y
Sbjct: 19 QDWHCDCFRCSVCSDSL-SNWYFEKDGKLYCRKDY 52
>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma
subfamily with unknown function. The third LIM domain
of an Enigma subfamily with unknown function: The Enigma
LIM domain family is comprised of three characterized
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
They serve as adaptor proteins, where the PDZ domain
tethers the protein to the cytoskeleton and the LIM
domains, recruit signaling proteins to implement
corresponding functions. The members of the enigma
family have been implicated in regulating or organizing
cytoskeletal structure, as well as involving multiple
signaling pathways. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 33.7 bits (77), Expect = 0.006
Identities = 13/32 (40%), Positives = 21/32 (65%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
N +H +CF C+ C+ +L GQ F ++ +PFC
Sbjct: 19 NNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFC 50
Score = 30.6 bits (69), Expect = 0.066
Identities = 17/52 (32%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C SC PI G R++ + ++H+ CF C C +L G+ F G C
Sbjct: 1 CVSCGFPIEA--GDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFC 50
>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 = 33.5 bits (77), Expect = 0.006
Identities = 14/52 (26%), Positives = 26/52 (50%), Gaps = 4/52 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C C I G+ + D++ H +CF+CA C +L +G+ +++ C
Sbjct: 1 CDKCGNGIVGV----VVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYC 48
Score = 25.4 bits (56), Expect = 4.0
Identities = 10/33 (30%), Positives = 20/33 (60%)
Query: 94 KNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
+++ H ECF C++C +L + + ED+ +C
Sbjct: 16 RDKNRHPECFVCADCGLNLKNKGYFFIEDELYC 48
>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 = 33.4 bits (76), Expect = 0.007
Identities = 14/34 (41%), Positives = 21/34 (61%), Gaps = 1/34 (2%)
Query: 158 DRHWHNDCFMCASCQSSLVGRGFITDGEDIICPD 191
DRHWH+ C C+ CQ+ L + F + G+ + C D
Sbjct: 21 DRHWHSKCLKCSDCQTQLAEKCF-SRGDSVYCKD 53
Score = 29.9 bits (67), Expect = 0.12
Identities = 16/33 (48%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH +C CS+C T LA + F SR D +C D F
Sbjct: 24 WHSKCLKCSDCQTQLAEKCF-SRGDSVYCKDDF 55
Score = 29.1 bits (65), Expect = 0.24
Identities = 13/31 (41%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYC 36
R WH KC C C+T + K F R +YC
Sbjct: 22 RHWHSKCLKCSDCQTQLAEKCF-SRGDSVYC 51
>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 = 32.8 bits (75), Expect = 0.009
Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C K I G R++ R +H + F C+ C+ L GF + I CP C
Sbjct: 1 CAQCNKIIRG----RYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKC 51
Score = 25.5 bits (56), Expect = 4.3
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R +H + F C CK + F + I+C CY
Sbjct: 18 RSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the
Paxillin-like protein family. The fourth LIM domain of
the Paxillin like protein family: This family consists
of paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 33.1 bits (76), Expect = 0.009
Identities = 16/47 (34%), Positives = 24/47 (51%)
Query: 84 QIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+ IT +T +H E F C+ C L+ F ++DKP+C CF
Sbjct: 6 KPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52
Score = 30.4 bits (69), Expect = 0.078
Identities = 19/55 (34%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C KPITG R I+ R +H + F+CA C L F + C C
Sbjct: 1 CAGCGKPITG----RCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPC 51
>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 = 32.9 bits (75), Expect = 0.009
Identities = 11/34 (32%), Positives = 18/34 (52%)
Query: 97 PWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
PWH+ CF C+ C SL ++ + +C C+
Sbjct: 20 PWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 31.8 bits (72), Expect = 0.026
Identities = 12/33 (36%), Positives = 18/33 (54%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH+ CF C C + + + ++ EIYC CY
Sbjct: 21 WHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 25.2 bits (55), Expect = 5.9
Identities = 12/32 (37%), Positives = 14/32 (43%)
Query: 161 WHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
WH +CF CA C SL +I C C
Sbjct: 21 WHKNCFRCAKCGKSLESTTLADKDGEIYCKGC 52
>gnl|CDD|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein
3 (CRP3/MLP). The first LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2
and CRP3 share a conserved nuclear targeting signal
(K/R-K/R-Y-G-P-K), which supports the fact that these
proteins function not only in the cytoplasm but also in
the nucleus. CRPs control regulatory pathways during
cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network.CRP3 also called Muscle LIM Protein (MLP),
which is a striated muscle-specific factor that
enhances myogenic differentiation. CRP3/MLP interacts
with cytoskeletal protein beta-spectrin. CRP3/MLP also
interacts with the basic helix-loop-helix myogenic
transcriptio n factors MyoD, myogenin, and MRF4 thereby
increasing their affinity for specific DNA regulatory
elements. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 32.0 bits (72), Expect = 0.019
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R +H+ CF C+ C+ + + + E EIYC CY
Sbjct: 20 RSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54
>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 = 0.025
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 141 CKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDCAK 194
C + GI GT + D+ +H +CFMC C +L RG+ E + C AK
Sbjct: 1 CTRCGNGIVGT-IVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYCETHAK 53
Score = 24.9 bits (54), Expect = 8.4
Identities = 9/36 (25%), Positives = 21/36 (58%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
V +++ +H ECF C +C +L + + +++ +C
Sbjct: 13 VKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
>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 = 31.9 bits (72), Expect = 0.026
Identities = 11/35 (31%), Positives = 20/35 (57%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH+ CF C +C + + + ++ E+YC CY
Sbjct: 19 KPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
Score = 31.5 bits (71), Expect = 0.035
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 96 EPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+PWH+ CF C+ C SL T ++ + +C C+
Sbjct: 19 KPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
>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 = 31.6 bits (72), Expect = 0.027
Identities = 14/39 (35%), Positives = 22/39 (56%)
Query: 88 SGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
G T ++ +H CFTC C +L G+ F + + KP+C
Sbjct: 12 GSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYC 50
>gnl|CDD|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred
partner (LPP). The second LIM domain of lipoma
preferred partner (LPP): LPP is a member of the zyxin
LIM protein family and contains three LIM zinc-binding
domains at the C-terminal and proline-rich region at the
N-terminal. LPP initially identified as the most
frequent translocation partner of HMGA2 (High Mobility
Group A2) in a subgroup of benign tumors of adipose
tissue (lipomas). It was also shown to be rearranged in
a number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP),Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 60
Score = 31.7 bits (72), Expect = 0.030
Identities = 17/43 (39%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 96 EPWHRECFTCSNCSTSLAGQRFT-SREDKPFCADCFGELFAKR 137
+P+H +CFTC C SL G FT ++ C + F + FA R
Sbjct: 18 KPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60
Score = 29.8 bits (67), Expect = 0.13
Identities = 15/43 (34%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 6 RQWHEKCFACVVC-KTPIGTKSFIPREQEIYCANCYEEKFATR 47
+ +H +CF CVVC K+ G + +I+C + +KFA R
Sbjct: 18 KPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60
>gnl|CDD|188800 cd09416, LIM2_Testin, The second LIM domain of Testin. The second
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. Testin is a cytoskeleton associated
focal adhesion protein that localizes along actin stress
fibers, at cell-cell-contact areas, and at focal
adhesion plaques. Testin interacts with a variety of
cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility and
adhesion events. Knockout mice experiments reveal that
tumor repressor function of testin. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 31.8 bits (72), Expect = 0.030
Identities = 14/37 (37%), Positives = 21/37 (56%)
Query: 94 KNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+N+ WH + F C +C LAG+ + DKP C C+
Sbjct: 19 ENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCY 55
>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 = 31.4 bits (71), Expect = 0.031
Identities = 12/32 (37%), Positives = 17/32 (53%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
++ WH+ CF C C L F S + KP+C
Sbjct: 18 DQTWHKACFHCEVCKMMLTVNNFVSHQKKPYC 49
Score = 29.1 bits (65), Expect = 0.20
Identities = 11/29 (37%), Positives = 18/29 (62%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYC 36
WH+ CF C VCK + +F+ +++ YC
Sbjct: 21 WHKACFHCEVCKMMLTVNNFVSHQKKPYC 49
>gnl|CDD|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein
1 (CRP1). The first LIM domain of Cysteine Rich
Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are
characterized by the presence of two LIM domains linked
to a short glycine-rich repeats (GRRs). The CRP family
members include CRP1, CRP2, CRP3/MLP and TLP. CRP1,
CRP2 and CRP3 share a conserved nuclear targeting
signal (K/R-K/R-Y-G-P-K), which supports the fact that
these proteins function not only in the cytoplasm but
also in the nucleus. CRPs control regulatory pathways
during cellular differentiation, and involve in complex
transcription circuits, and the organization as well as
the arrangement of the myofibrillar/cytoskeletal
network. CRP1 can associate with the actin cytoskeleton
and are capable of interacting with alpha-actinin and
zyxin. CRP1 was shown to regulate actin filament
bundling by interaction with alpha-actinin and direct
binding to actin filaments. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 31.5 bits (71), Expect = 0.035
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R +H+ CF C+VCK + + + +EIYC +CY
Sbjct: 21 RSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCY 55
Score = 25.7 bits (56), Expect = 4.0
Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 3/57 (5%)
Query: 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
K+C C+K + + E R +H CF+C C+ +L GE+I C C
Sbjct: 1 KKCGVCQKTVYF---AEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSC 54
Score = 25.0 bits (54), Expect = 8.6
Identities = 9/34 (26%), Positives = 16/34 (47%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCFG 131
+H+ CF C C +L ++ +C C+G
Sbjct: 23 FHKSCFLCMVCKKNLDSTTVAVHGEEIYCKSCYG 56
>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 = 31.2 bits (71), Expect = 0.038
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C + + G R I + +WH DCF C C L GF+ + +C C
Sbjct: 1 CGKCGEFVIG----RVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51
Score = 31.2 bits (71), Expect = 0.043
Identities = 12/35 (34%), Positives = 15/35 (42%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
N WH +CF C C+ LA F + C C
Sbjct: 17 NNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51
>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein
(CRP). The first LIM domain of Cysteine Rich Protein
(CRP): Cysteine-rich proteins (CRPs) are characterized
by the presence of two LIM domains linked to a short
glycine-rich repeats (GRRs). The CRP family members
include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share
a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function
not only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
control, and the organization as well as the
arrangement of the myofibrillar/cytoskeletal network.
It is evident that CRP1, CRP2, and CRP3/MLP are
involved in promoting protein assembly along the
actin-based cytoskeleton. Although members of the CRP
family share common binding partners, they are also
capable of recognizing different and specific targets.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 53
Score = 31.1 bits (70), Expect = 0.039
Identities = 14/35 (40%), Positives = 22/35 (62%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R +H+ CF C+VC+ + + + E EIYC +CY
Sbjct: 19 RSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCKSCY 53
>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 = 31.3 bits (71), Expect = 0.040
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH ECF CS+C F + +P C
Sbjct: 20 WHPECFVCSDCLKPFTDGSFFELDGRPLC 48
Score = 27.5 bits (61), Expect = 0.82
Identities = 11/44 (25%), Positives = 19/44 (43%), Gaps = 4/44 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFI 181
C C +P+ ++S + WH +CF+C+ C F
Sbjct: 1 CSGCGRPVK----ENYLSAANGVWHPECFVCSDCLKPFTDGSFF 40
Score = 26.7 bits (59), Expect = 1.8
Identities = 10/29 (34%), Positives = 12/29 (41%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYC 36
WH +CF C C P SF + C
Sbjct: 20 WHPECFVCSDCLKPFTDGSFFELDGRPLC 48
>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein
2 (CRP2). The first LIM domain of Cysteine Rich
Protein 2 (CRP2): The CRP family members include CRP1,
CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a
conserved nuclear targeting signal (K/R-K/R-Y-G-P-K),
which supports the fact that these proteins function
not only in the cytoplasm but also in the nucleus. CRPs
control regulatory pathways during cellular
differentiation, and involve in complex transcription
circuits, and the organization as well as the
arrangement of the myofibrillar/cytoskeletal network.
CRP2 specifically binds to protein inhibitor of
activated STAT-1 (PIAS1) and a novel human protein
designed CRP2BP (for CRP2 binding partner). PIAS1
specifically inhibits the STAT-1 pathway and CRP2BP is
homologous to members of the histone acetyltransferase
family raising the possibility that CRP2 is a modulator
of cytokine-controlled pathways or is functionally
active in the transcriptional regulatory network. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 55
Score = 31.1 bits (70), Expect = 0.042
Identities = 14/35 (40%), Positives = 23/35 (65%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R +H+ CF C+VC+ + + + +QEIYC +CY
Sbjct: 20 RSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCKSCY 54
>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b. The first
LIM domain of Lmx1b: Lmx1b belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In mouse, Lmx1b functions in the developing limbs and
eyes, the kidneys, the brain, and in cranial
mesenchyme. The disruption of Lmx1b gene results kidney
and limb defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 30.8 bits (70), Expect = 0.050
Identities = 14/36 (38%), Positives = 23/36 (63%), Gaps = 1/36 (2%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYE 41
R WHE+C C VC+ P+ T + R++++YC Y+
Sbjct: 19 RSWHEECLQCSVCQQPLTTSCYF-RDRKLYCKQDYQ 53
Score = 25.0 bits (55), Expect = 5.7
Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 5/48 (10%)
Query: 138 CYSCKKPITGIGGTRFI-SFEDRHWHNDCFMCASCQSSLVGRGFITDG 184
C C++PI+ R++ +R WH +C C+ CQ L + D
Sbjct: 1 CAGCQRPIS----DRYLLRVNERSWHEECLQCSVCQQPLTTSCYFRDR 44
>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH). The
first LIM domain of Arrowhead (AWH): Arrowhead belongs
to the LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Members of LHX family are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. During embryogenesis of
Drosophila, Arrowhead is expressed in each abdominal
segment and in the labial segment. Late in embryonic
development, expression of arrowhead is refined to the
abdominal histoblasts and salivary gland imaginal ring
cells themselves. The Arrowhead gene required for
establishment of a subset of imaginal tissues: the
abdominal histoblasts and the salivary gland imaginal
rings. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 54
Score = 30.8 bits (70), Expect = 0.053
Identities = 14/37 (37%), Positives = 22/37 (59%), Gaps = 1/37 (2%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTK-SFIPREQEIYC 36
++ R WH C C VC+TP+ + S R+++IYC
Sbjct: 14 LKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYC 50
>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 = 30.6 bits (69), Expect = 0.061
Identities = 13/34 (38%), Positives = 16/34 (47%)
Query: 7 QWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH +CF C C TP SF + + YC Y
Sbjct: 19 LWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHY 52
Score = 30.6 bits (69), Expect = 0.066
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
N WH ECF C C T F + +P+C
Sbjct: 17 NTLWHPECFVCRECFTPFVNGSFFEHDGQPYC 48
Score = 28.3 bits (63), Expect = 0.43
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
C C + I +IS + WH +CF+C C + V F
Sbjct: 1 CGGCARAIL----ENYISALNTLWHPECFVCRECFTPFVNGSF 39
>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 = 30.7 bits (70), Expect = 0.061
Identities = 14/39 (35%), Positives = 18/39 (46%), Gaps = 11/39 (28%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSR------EDKPFCADCF 130
WHRECF C+ C G F +DKP+C +
Sbjct: 24 WHRECFVCTTC-----GCPFQFSVPCYVLDDKPYCQQHY 57
Score = 27.6 bits (62), Expect = 0.83
Identities = 11/35 (31%), Positives = 15/35 (42%), Gaps = 1/35 (2%)
Query: 7 QWHEKCFACVVCKTPI-GTKSFIPREQEIYCANCY 40
QWH +CF C C P + + + YC Y
Sbjct: 23 QWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57
>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 = 30.5 bits (69), Expect = 0.062
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 1/33 (3%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WHE+C C CK P+ T F R++++YC Y
Sbjct: 21 WHERCLQCASCKEPLETTCFY-RDKKLYCKEDY 52
>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog
(ENH) family. The second LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 30.8 bits (69), Expect = 0.066
Identities = 14/35 (40%), Positives = 16/35 (45%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH CF CV C PI F + E YC Y
Sbjct: 18 QTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 25.4 bits (55), Expect = 4.8
Identities = 9/31 (29%), Positives = 14/31 (45%)
Query: 96 EPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
+ WH CF C C + F + +P+C
Sbjct: 18 QTWHVSCFVCVACHNPIRNNVFHLEDGEPYC 48
>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 = 30.7 bits (69), Expect = 0.068
Identities = 14/27 (51%), Positives = 15/27 (55%)
Query: 158 DRHWHNDCFMCASCQSSLVGRGFITDG 184
DRHWH+ C CA CQ L R F G
Sbjct: 18 DRHWHSSCLKCADCQMQLAERCFSRAG 44
Score = 26.5 bits (58), Expect = 1.9
Identities = 10/31 (32%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYC 36
R WH C C C+ + + F R +YC
Sbjct: 19 RHWHSSCLKCADCQMQLAERCF-SRAGNVYC 48
>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 = 30.9 bits (70), Expect = 0.069
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELF 134
++ +H+ CF CS+C +L ++S E +C F +LF
Sbjct: 18 LSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61
Score = 24.7 bits (54), Expect = 9.0
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKF 44
+H+ CF C CK + ++ E +YC +E+ F
Sbjct: 23 VVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61
>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 = 30.7 bits (69), Expect = 0.072
Identities = 12/36 (33%), Positives = 20/36 (55%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
VT + WH E F C++C + + F R+ +P+C
Sbjct: 14 VTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYC 49
Score = 30.4 bits (68), Expect = 0.090
Identities = 15/43 (34%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
C +CKKPI G + ++ + WH + F+C CQ + R F
Sbjct: 2 CGACKKPIAG----QVVTAMGKTWHPEHFVCTHCQEEIGSRNF 40
Score = 30.4 bits (68), Expect = 0.091
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH + F C C+ IG+++F R+ + YC Y
Sbjct: 19 KTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDY 53
>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating
Proteins. The first LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 55
Score = 30.0 bits (68), Expect = 0.097
Identities = 12/38 (31%), Positives = 13/38 (34%), Gaps = 3/38 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175
C CK+ IT WH CF C C L
Sbjct: 1 CVGCKESITE---GHAYELGGDRWHIHCFKCYKCDKKL 35
Score = 26.2 bits (58), Expect = 3.0
Identities = 7/15 (46%), Positives = 7/15 (46%)
Query: 98 WHRECFTCSNCSTSL 112
WH CF C C L
Sbjct: 21 WHIHCFKCYKCDKKL 35
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
The PINCH LIM4 domain recognizes the third SH3 domain of
another adaptor protein, Nck2. This step is an important
component of integrin signaling event. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the assem
bly of multimeric protein complexes.
Length = 54
Score = 30.0 bits (68), Expect = 0.098
Identities = 14/41 (34%), Positives = 24/41 (58%), Gaps = 4/41 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGR 178
C +C++PI G R ++ +HWH + F+CA C+ +G
Sbjct: 3 CGACRRPIEG----RVVTALGKHWHVEHFVCAKCEKPFLGH 39
Score = 29.2 bits (66), Expect = 0.18
Identities = 12/44 (27%), Positives = 18/44 (40%)
Query: 83 FQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
+ I VT + WH E F C+ C G R ++ +C
Sbjct: 7 RRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYC 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 = 30.0 bits (68), Expect = 0.12
Identities = 14/45 (31%), Positives = 19/45 (42%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFA 135
V E +H +CF C+ C F E + +C F LFA
Sbjct: 15 VNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
Score = 29.6 bits (67), Expect = 0.18
Identities = 13/38 (34%), Positives = 18/38 (47%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFA 45
+HE+CF C C P F E YC + ++ FA
Sbjct: 22 YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
>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 = 29.8 bits (67), Expect = 0.12
Identities = 16/54 (29%), Positives = 24/54 (44%), Gaps = 4/54 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPD 191
C SC+KPI G + ++ + WH + F+C C L R F C +
Sbjct: 3 CASCQKPIAG----QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEE 52
Score = 29.1 bits (65), Expect = 0.25
Identities = 11/35 (31%), Positives = 17/35 (48%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH + F C C +G++ F R + YC Y
Sbjct: 20 QTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54
Score = 27.9 bits (62), Expect = 0.62
Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 5/43 (11%)
Query: 84 QIITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
Q++T+ G T WH E F C C L + F R + +C
Sbjct: 13 QVVTALGQT-----WHPEHFVCCQCGKELGSRPFFERNGQAYC 50
>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 = 29.9 bits (67), Expect = 0.14
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH+ CF C C +L + + KP+C
Sbjct: 21 WHKACFHCEVCKMTLNMNNYKGYQKKPYC 49
Score = 29.2 bits (65), Expect = 0.24
Identities = 10/29 (34%), Positives = 17/29 (58%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYC 36
WH+ CF C VCK + ++ +++ YC
Sbjct: 21 WHKACFHCEVCKMTLNMNNYKGYQKKPYC 49
>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 = 29.8 bits (67), Expect = 0.14
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 7 QWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+WH+ CF C +C + + + E E+YC C+
Sbjct: 21 KWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQCH 54
Score = 25.5 bits (56), Expect = 4.8
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
WH+ CF C C+ L E + +C C
Sbjct: 22 WHKMCFKCGMCNKLLDSTNCAEHEGELYCKQC 53
>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule
interacting with CasL) like family. The LIM domain of
Mical (molecule interacting with CasL) like family:
Known members of this family includes LIM domain
containing proteins; Mical (molecule interacting with
CasL), pollen specific protein SF3, Eplin, xin
actin-binding repeat-containing protein 2 (XIRP2) and
Ltd-1. The members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth and mobility. Eplin has
also found to be tumor suppressor. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs.. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 29.5 bits (67), Expect = 0.15
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 97 PWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
+H+ CF CS+C+ +L + S E K +C
Sbjct: 20 LFHKSCFRCSHCNKTLRLGNYASLEGKLYC 49
Score = 25.7 bits (57), Expect = 3.2
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCAN 38
+H+ CF C C + ++ E ++YC
Sbjct: 21 FHKSCFRCSHCNKTLRLGNYASLEGKLYCKP 51
>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only
protein 2). The second LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex that
is capable of transcriptional activation. LMOs have also
been shown to be involved in oncogenesis. LMO1 and LMO2
are activated in T-cell acute lymphoblastic leukemia by
distinct chromosomal translocations. LMO2 was also shown
to be involved in erythropoiesis and is required for the
hematopoiesis in the adult animals. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 29.6 bits (66), Expect = 0.19
Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 3/53 (5%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL-VGRGFITDGEDIIC 189
C SC K I T + +D+ +H +CF CA+CQ VG ++ DI+C
Sbjct: 1 CASCDKRIRAYEMT--MRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 51
>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 = 29.4 bits (66), Expect = 0.20
Identities = 15/45 (33%), Positives = 22/45 (48%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
I +T ++ WH E F CS+C + F R+ KP+C F
Sbjct: 8 ILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
Score = 25.2 bits (55), Expect = 5.8
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 4/52 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C C PI ++ D+ WH + F C+ C GF+ C
Sbjct: 1 CAYCAGPIL----QNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYC 48
>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The first LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 57
Score = 29.2 bits (66), Expect = 0.20
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 4/49 (8%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGED 186
C C KPITG +F+ +H DCF C C + + F D D
Sbjct: 1 CAKCGKPITG----QFVRALGDVYHLDCFTCHDCGKPVASKFFPVDDPD 45
>gnl|CDD|188795 cd09411, LIM4_Paxillin, The fourth LIM domain of Paxillin. The
fourth LIM domain of Paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 29.1 bits (65), Expect = 0.25
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
IT +T + +H E F C+ C L F + DKP+C +CF
Sbjct: 8 ITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52
Score = 27.2 bits (60), Expect = 0.95
Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C C+KPITG R I+ + +H + F+CA C L F + C +C
Sbjct: 1 CSGCQKPITG----RCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNC 51
>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known
as Lim1) and Lhx5. The first LIM domain of Lhx1 (also
known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely
related members of LHX protein family, which features
two tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx1 is required
for regulating the vertebrate head organizer, the
nervous system, and female reproductive tract
development. During embryogenesis in the mouse, Lhx1 is
expressed early in mesodermal tissue, then later during
urogenital, kidney, liver, and nervous system
development. In the adult, expression is restricted to
the kidney and brain. A mouse embryos with Lhx1 gene
knockout cannot grow normal anterior head structures,
kidneys, and gonads, but with normally developed trunk
and tail morphology. In the developing nervous system,
Lhx1 is required to direct the trajectories of motor
axons in the limb. Lhx1 null female mice lack the
oviducts and uterus. Lhx5 protein may play
complementary or overlapping roles with Lhx1. The
expression of Lhx5 in the anterior portion of the mouse
neural tube suggests a role in patterning of the
forebrain. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 52
Score = 28.5 bits (64), Expect = 0.31
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 1/33 (3%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCAN 38
R WH KC C CK P+ K F RE ++YC N
Sbjct: 19 RAWHAKCVQCCDCKCPLTEKCF-SREGKLYCRN 50
Score = 28.2 bits (63), Expect = 0.44
Identities = 13/34 (38%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 97 PWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH +C C +C L + F SRE K +C + F
Sbjct: 20 AWHAKCVQCCDCKCPLTEKCF-SREGKLYCRNDF 52
Score = 26.6 bits (59), Expect = 1.6
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 138 CYSCKKPITGIGGTRFI-SFEDRHWHNDCFMCASCQSSLVGRGFITDGE 185
C C +PI +F+ + DR WH C C C+ L + F +G+
Sbjct: 1 CAGCDRPIL----DKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSREGK 45
>gnl|CDD|188837 cd09453, LIM1_ENH, The first LIM domain of the Enigma Homolog
(ENH) family. The first LIM domain of the Enigma
Homolog (ENH) family: ENH was initially identified in
rat brain. Same as enigma, it contains three LIM
domains at the C-terminus and a PDZ domain at
N-terminus. ENH is implicated in signal transduction
processes involving protein kinases. It has also been
shown that ENH interacts with protein kinase D1 (PKD1)
via its LIM domains and forms a complex with PKD1 and
the alpha1C subunit of cardiac L-type voltage-gated
calcium channel in rat neonatal cardiomyocytes. The
N-terminal PDZ domain interacts with alpha-actinin at
the Z-line. ENH is expressed in multiple tissues, such
as skeletal muscle, heart, bone, and brain. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 52
Score = 28.4 bits (63), Expect = 0.36
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
+ WH + F C CK+ + F+ + +YC CY
Sbjct: 18 KSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52
Score = 28.4 bits (63), Expect = 0.38
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 4/55 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIICPDC 192
C +C + I G F+ + WH + F CA C+SS+ GF+ + + C C
Sbjct: 1 CATCNQVIRG----PFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEIC 51
Score = 27.3 bits (60), Expect = 1.0
Identities = 11/33 (33%), Positives = 18/33 (54%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH E F C++C +S+A F + +C C+
Sbjct: 20 WHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52
>gnl|CDD|150282 pfam09554, RE_HaeII, HaeII restriction endonuclease. This family
includes the HaeII (recognises and cleaves RGCGC^Y)
restriction endonuclease.
Length = 338
Score = 31.0 bits (70), Expect = 0.36
Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 11/73 (15%)
Query: 33 EIYCANCYEEKFA------TRCVKCNKTFFRLRE-KGTFQSHSG---RINKVYSILFYFL 82
E Y + E+F+ C+ K F+L E F G I+K+Y I+ Y L
Sbjct: 99 EAYIYKKFFERFSQMSSALAYCLTSTKENFKLSEFLNQFWLEPGLKRSIDKIYEIVVYAL 158
Query: 83 FQ-IITSGGVTYK 94
F+ +I GV K
Sbjct: 159 FEVLIEELGVKVK 171
>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin. The
fourth LIM domain of Leupaxin: Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. Leupaxin belongs to
the paxillin focal adhesion protein family. Same as
other members of the family, it has four leucine-rich
LD-motifs in the N-terminus and four LIM domains in the
C-terminus. It may function in cell type-specific
signaling by associating with interaction partners PYK2,
FAK, PEP and p95PKL. When expressed in human leukocytic
cells, leupaxin significantly suppressed
integrin-mediated cell adhesion to fibronectin and the
tyrosine phosphorylation of paxillin. These findings
indicate that leupaxin may negatively regulate the
functions of paxillin during integrin signaling. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 28.5 bits (64), Expect = 0.40
Identities = 16/34 (47%), Positives = 19/34 (55%), Gaps = 4/34 (11%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASC 171
C SC PITG R IS R +H + F+CA C
Sbjct: 1 CGSCGLPITG----RCISALGRKFHPEHFVCAFC 30
Score = 27.8 bits (62), Expect = 0.74
Identities = 14/45 (31%), Positives = 21/45 (46%)
Query: 86 ITSGGVTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
IT ++ +H E F C+ C L F + KP+C+ CF
Sbjct: 8 ITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
Score = 24.7 bits (54), Expect = 9.0
Identities = 11/35 (31%), Positives = 19/35 (54%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R++H + F C C P+ SF + + YC+ C+
Sbjct: 18 RKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX
protein family. The second LIM domain of Isl: Isl is a
member of LHX protein family, which features two tandem
N-terminal LIM domains and a C-terminal DNA binding
homeodomain. Isl1 and Isl2 are the two conserved members
of this family. Proteins in this group are found in the
nucleus and act as transcription factors or cofactors.
LHX proteins are critical for the development of
specialized cells in multiple tissue types, including
the nervous system, skeletal muscle, the heart, the
kidneys, and endocrine organs, such as the pituitary
gland and the pancreas. Isl-1 is one of the LHX proteins
isolated originally by virtue of its ability to bind DNA
sequences from the 5'-flanking region of the rat insulin
gene in pancreatic insulin-producing cells. Mice
deficient in Isl-1 fail to form the dorsal exocrine
pancreas and islet cells fail to differentiate. On the
other hand, Isl-1 takes part in the pituitary
development by activating the gonadotropin-releasing
hormone receptor gene together with LHX3 and
steroidogenic factor 1. Mouse Isl2 is expressed in the
retinal ganglion cells and the developing spinal cord
where it plays a role in motor neuron development. Same
as Isl1, Isl2 may also be able to bind to the insulin
gene enhancer to promote gene activation. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 28.2 bits (63), Expect = 0.44
Identities = 15/34 (44%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 94 KNEPWHRECFTCSNCSTSL-AGQRFTSREDKPFC 126
+ + +H ECF CS CS L G F R+D FC
Sbjct: 18 RTKIYHIECFRCSACSRQLIPGDEFALRDDGLFC 51
Score = 24.7 bits (54), Expect = 9.3
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 1 MEYKTRQWHEKCFACVVC-KTPIGTKSFIPREQEIYC 36
M +T+ +H +CF C C + I F R+ ++C
Sbjct: 15 MRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFC 51
>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 = 28.2 bits (63), Expect = 0.45
Identities = 14/52 (26%), Positives = 21/52 (40%), Gaps = 2/52 (3%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C C K + G + +H +CF C SC +L G+ F + C
Sbjct: 1 CVKCGKGVYGAS--QACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYC 50
Score = 27.0 bits (60), Expect = 1.2
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
+H CFTC +C +L G+ F + K +C + +
Sbjct: 22 YHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin
like protein family. The second LIM domain of the
paxillin like protein family: This family consists of
paxillin, leupaxin, Hic-5 (ARA55), and other related
proteins. There are four LIM domains in the C-terminal
of the proteins and leucine-rich LD-motifs in the
N-terminal region. Members of this family are adaptor
proteins to recruit key components of
signal-transduction machinery to specific sub-cellular
locations. Paxillin is found at the interface between
the plasma membrane and the actin cytoskeleton. Paxillin
serves as a platform for the recruitment of numerous
regulatory and structural proteins that together control
the dynamic changes in cell adhesion, cytoskeletal
reorganization and gene expression that are necessary
for cell migration and survival. Leupaxin is a
cytoskeleton adaptor protein, which is preferentially
expressed in hematopoietic cells. It associates with
focal adhesion kinases PYK2 and pp125FAK and identified
to be a component of the osteoclast pososomal signaling
complex. Hic-5 controls cell proliferation, migration
and senescence by functioning as coactivator for steroid
receptors such as androgen receptor, glucocorticoid
receptor and progesterone receptor. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 28.1 bits (63), Expect = 0.46
Identities = 12/40 (30%), Positives = 21/40 (52%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
VT ++ WH E F C+ C + F ++ KP+C + +
Sbjct: 13 VTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 27.4 bits (61), Expect = 1.0
Identities = 11/33 (33%), Positives = 16/33 (48%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH + F C C P G + F ++ + YC Y
Sbjct: 20 WHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 25.4 bits (56), Expect = 5.1
Identities = 13/43 (30%), Positives = 18/43 (41%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
C C PI + ++ D+ WH + F CA C GF
Sbjct: 1 CAYCNGPILD----KCVTALDKTWHPEHFFCAQCGKPFGDEGF 39
>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 = 28.3 bits (63), Expect = 0.46
Identities = 11/25 (44%), Positives = 14/25 (56%)
Query: 161 WHNDCFMCASCQSSLVGRGFITDGE 185
WHN CF C+ CQ L + DG+
Sbjct: 21 WHNSCFQCSVCQDLLTNWYYEKDGK 45
Score = 27.5 bits (61), Expect = 0.86
Identities = 11/32 (34%), Positives = 15/32 (46%), Gaps = 1/32 (3%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
E WH CF CS C L + ++ K +C
Sbjct: 18 QEAWHNSCFQCSVCQDLLTNWYY-EKDGKLYC 48
Score = 24.8 bits (54), Expect = 8.6
Identities = 11/33 (33%), Positives = 18/33 (54%), Gaps = 1/33 (3%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH CF C VC+ + T + ++ ++YC Y
Sbjct: 21 WHNSCFQCSVCQDLL-TNWYYEKDGKLYCHKHY 52
>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP,
actinin-associated LIM protein. This family represents
the LIM domain of ALP, actinin-associated LIM protein.
ALP contains an N-terminal PDZ domain, a C-terminal LIM
domain and an ALP-subfamily-specific 34-amino-acid motif
termed ALP-like motif (AM), which contains a putative
consensus protein kinase C (PKC) phosphorylation site
and two alpha-helices. ALP proteins are found in heart
and in skeletal muscle. ALP may act as a signaling
molecule which is regulated by PKC-dependent signaling.
ALP plays an essential role in the development of RV
(right ventricle) chamber. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 27.9 bits (62), Expect = 0.52
Identities = 16/46 (34%), Positives = 27/46 (58%), Gaps = 2/46 (4%)
Query: 141 CKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRG-FITDGE 185
C K +GI GT + D++ H +CF+C+ C +L +G F +G+
Sbjct: 1 CDKCGSGIVGT-VVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQ 45
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 28.0 bits (62), Expect = 0.54
Identities = 15/43 (34%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGF 180
CY C PI + ++ DR WH + F CA C + GF
Sbjct: 1 CYYCNGPIL----DKVVTALDRTWHPEHFFCAQCGAFFGPEGF 39
Score = 26.8 bits (59), Expect = 1.5
Identities = 11/36 (30%), Positives = 17/36 (47%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
VT + WH E F C+ C + F ++ K +C
Sbjct: 13 VTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYC 48
Score = 24.9 bits (54), Expect = 6.7
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
R WH + F C C G + F ++ + YC Y
Sbjct: 18 RTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only
protein 4). The first LIM domain of LMO4 (LIM domain
only protein 4): LMO4 is a nuclear protein that plays
important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact with
Smad proteins, and associate with the promoter of the
PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential role
for LMO4 as a negative regulator of BRCA1 in sporadic
breast cancer. LMO4 also forms complex to both ERa
(oestrogen receptor alpha), MTA1 (metastasis tumor
antigen 1), and HDACs (histone deacetylases), implying
that LMO4 is also a component of the MTA1 corepressor
complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 55
Score = 28.2 bits (63), Expect = 0.55
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 158 DRHWHNDCFMCASCQSSL--VGRGFITDGEDIIC 189
DR+WHN C C+ CQ+ L +G T G I+C
Sbjct: 18 DRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILC 51
>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain
Kinase 1). The first LIM domain of LIMK1 (LIM domain
Kinase 1): LIMK1 belongs to the LIMK protein family,
which comprises LIMK1 and LIMK2. LIMK contains two LIM
domains, a PDZ domain, and a kinase domain. LIMK is
involved in the regulation of actin polymerization and
microtubule disassembly. LIMK influences architecture of
the actin cytoskeleton by regulating the activity of the
cofilin family proteins cofilin1, cofilin2, and destrin.
The mechanism of the activation is to phosphorylates
cofilin on serine 3 and inactivates its actin-severing
activity, and altering the rate of actin
depolymerization. LIMKs can function in both cytoplasm
and nucleus. Both LIMK1 and LIMK2 can act in the nucleus
to suppress Rac/Cdc42-dependent cyclin D1 expression.
LIMK1 is expressed in all tissues and is localized to
focal adhesions in the cell. LIMK1 can form homodimers
upon binding of HSP90 and is activated by Rho effector
Rho kinase and MAPKAPK2. LIMK1 is important for normal
central nervous system development, and its deletion has
been implicated in the development of the human genetic
disorder Williams syndrome. Moreover, LIMK1 up-regulates
the promoter activity of urokinase type plasminogen
activator and induces its mRNA and protein expression in
breast cancer cells. The LIM domains have been shown to
play an important role in regulating kinase activity and
likely also contribute to LIMK function by acting as
sites of protein-to-protein interactions. All LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 74
Score = 28.7 bits (64), Expect = 0.55
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
N WH +CF C C SL+ + ++ + FC
Sbjct: 39 NSDWHADCFRCCECGASLS-HWYYEKDGRLFC 69
Score = 27.9 bits (62), Expect = 0.83
Identities = 15/48 (31%), Positives = 22/48 (45%), Gaps = 3/48 (6%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGE 185
C SC + I +++ + WH DCF C C +SL + DG
Sbjct: 22 CASCGQ---SIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEKDGR 66
>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 = 28.1 bits (63), Expect = 0.56
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 1/52 (1%)
Query: 80 YFLFQIITSGGVTYKNEPWHRECFTCSNCSTSLAGQ-RFTSREDKPFCADCF 130
Y Q+I V+ N+ W + F+CS C T L + +F + KP C C+
Sbjct: 2 YHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCY 53
Score = 25.8 bits (57), Expect = 3.7
Identities = 12/38 (31%), Positives = 18/38 (47%), Gaps = 4/38 (10%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175
CY C + I G +S ++ W D F C+ C + L
Sbjct: 1 CYHCNQVIEG----DVVSALNKTWCVDHFSCSFCDTKL 34
Score = 24.6 bits (54), Expect = 8.6
Identities = 11/35 (31%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 8 WHEKCFACVVCKTPIGTKS-FIPREQEIYCANCYE 41
W F+C C T + KS F + + C CY+
Sbjct: 20 WCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKCYD 54
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. The consensus sequence of LIM domain
has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 28.2 bits (63), Expect = 0.63
Identities = 10/32 (31%), Positives = 14/32 (43%)
Query: 97 PWHRECFTCSNCSTSLAGQRFTSREDKPFCAD 128
+HR CF C+ C L F E +C +
Sbjct: 24 VYHRTCFKCARCGVQLTPGSFYETEYGSYCCE 55
Score = 27.8 bits (62), Expect = 0.81
Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL-VGRGFITDGEDIICPDC 192
C SC P+ + E + +H CF CA C L G + T+ C C
Sbjct: 5 CASCGLPVFL---AERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYCCETC 57
>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga GTPase-Activating
Proteins. The second LIM domain of Rga
GTPase-Activating Proteins: The members of this family
contain two tandem repeats of LIM domains and a Rho-type
GTPase activating protein (RhoGap) domain. Rga activates
GTPases during polarized morphogenesis. In yeast, a
known regulating target of Rga is CDC42p, a small
GTPase. The LIM domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 27.8 bits (62), Expect = 0.64
Identities = 9/35 (25%), Positives = 16/35 (45%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADC 129
+E + +CF C CS + ++ + FC C
Sbjct: 18 DEAYCSDCFRCRRCSRDITDLKYAKTKRGLFCMSC 52
>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 = 28.0 bits (62), Expect = 0.68
Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 1/49 (2%)
Query: 141 CKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C K +GI G F+ D+ H +C++C C ++L +G + I C
Sbjct: 1 CDKCGSGIVGV-FVKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYC 48
Score = 26.8 bits (59), Expect = 1.5
Identities = 12/36 (33%), Positives = 22/36 (61%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
V +++P H EC+ C++C T+L + ED+ +C
Sbjct: 13 VKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYC 48
>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 = 27.8 bits (62), Expect = 0.70
Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 6/43 (13%)
Query: 138 CYSCKKPITGIGGTRFISFE----DRHWHNDCFMCASCQSSLV 176
CY CK+P+ G + E D+ WH CF+C++C LV
Sbjct: 1 CYCCKQPMKE--GDPAVYAERAGYDKLWHPACFVCSTCGELLV 41
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription. Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 27.4 bits (61), Expect = 0.79
Identities = 10/27 (37%), Positives = 13/27 (48%)
Query: 158 DRHWHNDCFMCASCQSSLVGRGFITDG 184
DR WH C C C + L + F +G
Sbjct: 18 DRTWHAKCLKCNDCGAQLTDKCFARNG 44
Score = 26.6 bits (59), Expect = 1.5
Identities = 11/34 (32%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 97 PWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
WH +C C++C L + F +R +C D F
Sbjct: 20 TWHAKCLKCNDCGAQLTDKCF-ARNGHVYCKDDF 52
Score = 25.1 bits (55), Expect = 5.8
Identities = 12/31 (38%), Positives = 14/31 (45%), Gaps = 1/31 (3%)
Query: 6 RQWHEKCFACVVCKTPIGTKSFIPREQEIYC 36
R WH KC C C + K F R +YC
Sbjct: 19 RTWHAKCLKCNDCGAQLTDKCF-ARNGHVYC 48
>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM
domain only protein 1 and 3). The first LIM domain of
LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1
and LMO3 are highly homologous and belong to the LMO
protein family. LMO1 and LMO3 are nuclear protein that
plays important roles in transcriptional regulation and
development. As LIM domains lack intrinsic DNA-binding
activity, nuclear LMOs are involved in transcriptional
regulation by forming complexes with other transcription
factors or cofactors. For example, LMO1 interacts with
the the bHLH domain of bHLH transcription factor, TAL1
(T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1
inhibits the expression of TAL1/SCL target genes. LMO3
facilitates p53 binding to its response elements, which
suggests that LMO3 acts as a co-repressor of p53,
suppressing p53-dependent transcriptional regulation. In
addition, LMO3 interacts with neuronal transcription
factor, HEN2, and acts as an oncogene in neuroblastoma.
Another binding partner of LMO3 is calcium- and
integrin-binding protein CIB, which binds via the second
LIM domain (LIM2) of LMO3. One role of the CIB/LMO3
complex is to inhibit cell proliferation. Although LMO1
and LMO3 are highly homologous proteins, they play
different roles in the regulation of the pituitary
glycoprotein hormone alpha-subunit (alpha GSU) gene.
Alpha GSU promoter activity was markedly repressed by
LMO1 but activated by LMO3. All LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 27.5 bits (61), Expect = 0.80
Identities = 14/34 (41%), Positives = 17/34 (50%), Gaps = 2/34 (5%)
Query: 158 DRHWHNDCFMCASCQSSL--VGRGFITDGEDIIC 189
D++WH DC CA C L VG T I+C
Sbjct: 18 DQYWHEDCLKCACCDCRLGEVGSTLYTKANLILC 51
>gnl|CDD|187811 cd09680, Cas10_III, CRISPR/Cas system-associated protein Cas10.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Multidomain protein with permuted HD nuclease domain,
palm domain and Zn-ribbon; signature gene for type III;
also known as Csm1 family.
Length = 650
Score = 30.0 bits (68), Expect = 0.80
Identities = 8/50 (16%), Positives = 15/50 (30%), Gaps = 3/50 (6%)
Query: 15 CVVCKTPIGTKSFIPREQEIYCANCYEEKFATRCVKCNKTFFRLREKGTF 64
C VC + E E C C + + + +F ++
Sbjct: 395 CKVCGRE---EPIAEDEDEGLCPTCERLYELGKELLKDDSFLVTEKEDGG 441
>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal
Protein (CRIP). The LIM domain of Cysteine-Rich
Intestinal Protein (CRIP): CRIP is a short protein with
only one LIM domain. CRIP gene is developmentally
regulated and can be induced by glucocorticoid hormones
during the first three postnatal weeks. The domain shows
close sequence homology to LIM domain of thymus LIM
protein. However, unlike the TLP proteins which have two
LIM domains, the members of this family have only one
LIM domain. LIM domains are 50-60 amino acids in size
and share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 27.5 bits (61), Expect = 0.87
Identities = 12/36 (33%), Positives = 16/36 (44%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
VT + WHR C C C +L + KP+C
Sbjct: 14 VTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49
>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 = 27.6 bits (61), Expect = 0.90
Identities = 11/30 (36%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 8 WHEKCFACVVCKTPIGTK-SFIPREQEIYC 36
WH +C +C VC+T +G S ++++I+C
Sbjct: 22 WHVRCLSCSVCRTSLGRHTSCYIKDKDIFC 51
>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 = 27.4 bits (61), Expect = 0.92
Identities = 13/30 (43%), Positives = 15/30 (50%), Gaps = 1/30 (3%)
Query: 98 WHRECFTCSNCSTSLA-GQRFTSREDKPFC 126
+H +CFTCS C L G RF FC
Sbjct: 22 YHLKCFTCSTCHNQLVPGDRFHYVNGSLFC 51
>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting
with CasL). The LIM domain of Mical (molecule
interacting with CasL): MICAL is a large, multidomain,
cytosolic protein with a single LIM domain, a calponin
homology (CH) domain and a flavoprotein monooxygenase
domain. In Drosophila, MICAL is expressed in axons,
interacts with the neuronal A (PlexA) receptor and is
required for Semapho-rin 1a (Sema-1a)-PlexA-mediated
repulsive axon guidance. The LIM domain and calporin
homology domain are known for interactions with the
cytoskeleton, cytoskeletal adaptor proteins, and other
signaling proteins. The flavoprotein monooxygenase (MO)
is required for semaphorin-plexin repulsive axon
guidance during axonal pathfinding in the Drosophila
neuromuscular system. In addition, MICAL was
characterized to interact with Rab13 and Rab8 to
coordinate the assembly of tight junctions and adherens
junctions in epithelial cells. Thus, MICAL was also
named junctional Rab13-binding protein (JRAB). As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 55
Score = 27.3 bits (61), Expect = 0.92
Identities = 12/30 (40%), Positives = 15/30 (50%), Gaps = 2/30 (6%)
Query: 99 HRECFTCSNCSTSL--AGQRFTSREDKPFC 126
HR CF CS C T+L F + K +C
Sbjct: 22 HRSCFKCSYCGTTLRLGAYAFDRDDGKFYC 51
>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 = 27.3 bits (61), Expect = 0.98
Identities = 10/30 (33%), Positives = 15/30 (50%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFCA 127
WH+ CF C C +L + + KP+C
Sbjct: 21 WHKGCFKCEVCGMTLNMKNYKGYNKKPYCN 50
Score = 25.4 bits (56), Expect = 4.3
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCANCY 40
WH+ CF C VC + K++ ++ YC Y
Sbjct: 21 WHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53
>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein
SF3. The second Lim domain of pollen specific protein
SF3: SF3 is a Lim protein that is found exclusively in
mature plant pollen grains. It contains two LIM domains.
The exact function of SF3 is unknown. It may be a
transcription factor required for the expression of late
pollen genes. It is possible that SF3 protein is
involved in controlling pollen-specific processes such
as male gamete maturation, pollen tube formation, or
even fertilization. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein.
Length = 61
Score = 27.4 bits (61), Expect = 1.0
Identities = 11/47 (23%), Positives = 25/47 (53%)
Query: 91 VTYKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKR 137
VT + +H+ CF CS+ +++ + + E + +C +LF ++
Sbjct: 14 VTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60
>gnl|CDD|188822 cd09438, LIM3_Ajuba_like, The third LIM domain of Ajuba-like
proteins. The third LIM domain of Ajuba-like proteins:
Ajuba like LIM protein family includes three highly
homologous proteins Ajuba, Limd1, and WTIP. Members of
the family contain three tandem C-terminal LIM domains
and a proline-rich N-terminal region. This family of
proteins functions as scaffolds, participating in the
assembly of numerous protein complexes. In the
cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated
ERK activation. Ajuba also recruits the TNF
receptor-associated factor 6 (TRAF6) to p62 and
activates PKCKappa activity. Ajuba interacts with
alpha-catenin and F-actin to contribute to the formation
or stabilization of adheren junctions by linking
adhesive receptors to the actin cytoskeleton. Although
Ajuba is a cytoplasmic protein, it can shuttle into the
nucleus. In nucleus, Ajuba functions as a corepressor
for the zinc finger-protein Snail. It binds to the SNAG
repression domain of Snail through its LIM region.
Arginine methyltransferase-5 (Prmt5), a protein in the
complex, is recruited to Snai l through an interaction
with Ajuba. This ternary complex functions to repress
E-cadherin, a Snail target gene. In addition, Ajuba
contains functional nuclear-receptor interacting motifs
and selectively interacts with retinoic acid receptors
(RARs) and rexinoid receptor (RXRs) to negatively
regulate retinoic acid signaling. Wtip, the
Wt1-interacting protein, was originally identified as an
interaction partner of the Wilms tumour protein 1 (WT1).
Wtip is involved in kidney and neural crest development.
Wtip interacts with the receptor tyrosine kinase Ror2
and inhibits canonical Wnt signaling. LIMD1 was reported
to inhibit cell growth and metastases. The inhibition
may be mediated through an interaction with the protein
barrier-to-autointegration (BAF), a component of SWI/SNF
chromatin-remodeling protein; or through the interaction
with retinoblastoma protein (pRB), resulting in
inhibition of E2F-mediated transcription, and expression
of the majority of genes with E2F1- responsive elements.
Recently, Limd1 was shown to interact with the
p62/sequestosome protein and influence IL-1 and RANKL
signaling by facilitating the assembly of a
p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62
interaction affects both NF-kappaB and AP-1 activity in
epithelial cells and osteoclasts. Moreover, LIMD1
functions as tumor repressor to block lung tumor cell
line in vitro and in vivo. Recent studies revealed that
LIM proteins Wtip, LIMD1 and Ajuba interact with
components of RNA induced silencing complexes (RISC) as
well as eIF4E and the mRNA m7GTP cap-protein complex and
are required for microRNA-mediated gene silencing. As
in other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 62
Score = 27.4 bits (61), Expect = 1.1
Identities = 13/42 (30%), Positives = 21/42 (50%), Gaps = 5/42 (11%)
Query: 138 CYSCKKPITGIGGT----RFISFEDRHWHNDCFMCASCQSSL 175
C +C +PI G+ R +S D+ +H +C+ C C L
Sbjct: 1 CAACGQPILPAEGSEETIRVVSM-DKDYHVECYHCEDCGLQL 41
>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 = 27.0 bits (60), Expect = 1.2
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 5/50 (10%)
Query: 137 RCYSCKKPITGIGGTRFI-SFEDRHWHNDCFMCASCQSSLVGRGFITDGE 185
+C C PI RFI +D+ WH+ C C CQ+ L + F G+
Sbjct: 3 KCAGCDHPIF----DRFILKVQDKPWHSKCLKCVDCQAQLTDKCFSRGGQ 48
Score = 26.7 bits (59), Expect = 1.6
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 1/36 (2%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCF 130
++PWH +C C +C L + F SR + +C + F
Sbjct: 21 DKPWHSKCLKCVDCQAQLTDKCF-SRGGQVYCKEDF 55
>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 = 27.2 bits (61), Expect = 1.2
Identities = 16/43 (37%), Positives = 20/43 (46%), Gaps = 6/43 (13%)
Query: 138 CYSCKKPIT----GIGGTRFISFEDRHWHNDCFMCASCQSSLV 176
C CK+PI + R ED WH CF+C +C LV
Sbjct: 1 CEKCKEPINPGEVAVFAERAG--EDACWHPGCFVCETCNELLV 41
Score = 26.0 bits (58), Expect = 3.4
Identities = 9/29 (31%), Positives = 13/29 (44%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF C C+ L + + K +C
Sbjct: 26 WHPGCFVCETCNELLVDLIYFYHDGKIYC 54
Score = 24.9 bits (55), Expect = 7.1
Identities = 6/16 (37%), Positives = 7/16 (43%)
Query: 4 KTRQWHEKCFACVVCK 19
+ WH CF C C
Sbjct: 22 EDACWHPGCFVCETCN 37
>gnl|CDD|188716 cd09330, LIM4_abLIM, The fourth LIM domain of actin binding LIM
(abLIM) proteins. The fourth LIM domain of actin
binding LIM (abLIM) proteins: Three homologous members
of the abLIM protein family have been identified;
abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM
consists of four tandem repeats of LIM domains and the
C-terminal of acting binding LIM protein is a villin
headpiece domain, which has strong actin binding
activity. The abLIM-1, which is expressed in retina,
brain, and muscle tissue, has been indicated to function
as a tumor suppressor. AbLIM-2 and -3, mainly expressed
in muscle and neuronal tissue, bind to F-actin strongly.
They may serve as a scaffold for signaling modules of
the actin cytoskeleton and thereby modulate
transcription. It has shown that LIM domains of abLIMs
interact with STARS (striated muscle activator of Rho
signaling), which directly binds actin and stimulates
serum-response factor (SRF)-dependent transcription. All
LIM domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 56
Score = 26.9 bits (60), Expect = 1.3
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLV-GRGFITDGEDIICPDCAKAK 196
C +C K ITG + + +H+H C C+ C G G +I PDC +A
Sbjct: 1 CEACDKFITG----KVLEAGGKHYHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCRQAA 56
>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma
subfamily with unknown function. The first LIM domain
of an Enigma subfamily with unknown function: The Enigma
LIM domain family is comprised of three characterized
members: Enigma, ENH and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
They serve as adaptor proteins, where the PDZ domain
tethers the protein to the cytoskeleton and the LIM
domains, recruit signaling proteins to implement
corresponding functions. The members of the Enigma
family have been implicated in regulating or organizing
cytoskeletal structure, as well as involving multiple
signaling pathways. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 27.0 bits (60), Expect = 1.3
Identities = 19/57 (33%), Positives = 27/57 (47%), Gaps = 6/57 (10%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCA--SCQSSLVGRGFITDGEDIICPDC 192
C SC + I G FI+ + W D F+CA SC+ L GF+ + + C C
Sbjct: 1 CESCNQQIRG----PFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYC 53
>gnl|CDD|188719 cd09333, LIM3_PINCH, The third LIM domain of protein PINCH. The
third LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 51
Score = 26.6 bits (59), Expect = 1.6
Identities = 16/47 (34%), Positives = 23/47 (48%), Gaps = 10/47 (21%)
Query: 93 YKNEPWHRECFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCY 139
+K +P+H F C+NC L +RE K GEL+ RC+
Sbjct: 15 FKGDPYHPYHFNCANCGKELTA---DARELK-------GELYCLRCH 51
>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9
family. The first LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Although Lhx2 and Lhx9 are highly homologous, they
seems to play regulatory roles in different organs. In
animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. Lhx9 is expressed in several
regions of the developing mouse brain , the spinal
cord, the pancreas, in limb mesenchyme, and in the
urogenital region. Lhx9 plays critical roles in gonad
development. Homozygous mice lacking functional Lhx9
alleles exhibit numerous urogenital defects, such as
gonadal agenesis, infertility, and undetectable levels
of testosterone and estradiol coupled with high FSH
levels. Lhx9 null mice are phenotypically female, even
those that are genotypically male. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 54
Score = 26.5 bits (59), Expect = 1.7
Identities = 14/36 (38%), Positives = 19/36 (52%), Gaps = 1/36 (2%)
Query: 6 RQWHEKCFACVVCKTPIGTK-SFIPREQEIYCANCY 40
RQWH C C C+ P+ ++ S R+ IYC Y
Sbjct: 19 RQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>gnl|CDD|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only
protein 2). The first LIM domain of LMO2 (LIM domain
only protein 2): LMO2 is a nuclear protein that plays
important roles in transcriptional regulation and
development. The two tandem LIM domains of LMO2 support
the assembly of a crucial cell-regulatory complex by
interacting with both the TAL1-E47 and GATA1
transcription factors to form a DNA-binding complex that
is capable of transcriptional activation. LMOs have also
been shown to be involved in oncogenesis. LMO1 and LMO2
are activated in T-cell acute lymphoblastic leukemia by
distinct chromosomal translocations. LMO2 was also shown
to be involved in erythropoiesis and is required for the
hematopoiesis in the adult animals. All LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 26.4 bits (58), Expect = 2.2
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 3/38 (7%)
Query: 138 CYSCKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSL 175
C C++ IG F+ D++WH DC C C L
Sbjct: 1 CGGCQQ---NIGDRYFLKAIDQYWHEDCLSCDLCGCRL 35
>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 = 26.4 bits (58), Expect = 2.2
Identities = 13/29 (44%), Positives = 14/29 (48%)
Query: 161 WHNDCFMCASCQSSLVGRGFITDGEDIIC 189
WH CF CASCQ LV + I C
Sbjct: 26 WHPQCFQCASCQELLVDLIYFYQDGKIYC 54
>gnl|CDD|233895 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2,) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 28.5 bits (64), Expect = 2.4
Identities = 17/81 (20%), Positives = 28/81 (34%), Gaps = 8/81 (9%)
Query: 102 CFTCSNCSTSLAGQRFTSREDKPFCADCFGELFAKRCYSCKKPITGIGGTRFISFEDRHW 161
C CSN + +E++ C C + C + ++ + R R
Sbjct: 28 CKWCSNPESQRKSPELLFKENR--CLGCGK--CVEVCPAGTARLSELADGRNRIIIRREK 83
Query: 162 HNDCFMC-ASCQS---SLVGR 178
C C +C S S+VG
Sbjct: 84 CTHCGKCTEACPSGALSIVGE 104
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a role
in development of normal thymus and in controlling the
development and differentiation of thymic epithelial
cells. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 26.1 bits (57), Expect = 2.9
Identities = 9/29 (31%), Positives = 12/29 (41%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WHR C C C +L + P+C
Sbjct: 21 WHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein
(TLP). The first LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a
role in development of normal thymus and in controlling
the development and differentiation of thymic epithelial
cells. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 26.1 bits (57), Expect = 3.4
Identities = 11/29 (37%), Positives = 14/29 (48%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WHR C C CS L+ + KP+C
Sbjct: 21 WHRFCLKCERCSKILSPGGHAEHDGKPYC 49
>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 = 26.1 bits (58), Expect = 3.5
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 98 WHRECFTCSNCSTSL-AGQRFTSREDKPFC 126
+H CFTC+ C+ L G F R+ +C
Sbjct: 26 FHLNCFTCATCNKPLTKGDHFGMRDGLVYC 55
>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 = 25.8 bits (57), Expect = 3.6
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 1/36 (2%)
Query: 6 RQWHEKCFACVVCKTPI-GTKSFIPREQEIYCANCY 40
+ +H CF C VC + G + E IYC Y
Sbjct: 18 KSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53
>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 = 25.7 bits (56), Expect = 4.2
Identities = 12/36 (33%), Positives = 20/36 (55%), Gaps = 2/36 (5%)
Query: 7 QWHEKCFACVVCKTPI--GTKSFIPREQEIYCANCY 40
++H +CFAC+ CK I G + + +YC C+
Sbjct: 24 KYHPECFACMSCKVIIEDGDTYALVQHTTLYCGKCH 59
>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 = 25.4 bits (56), Expect = 4.4
Identities = 10/39 (25%), Positives = 20/39 (51%), Gaps = 2/39 (5%)
Query: 94 KNEPWHRECFTCSNCSTSLA--GQRFTSREDKPFCADCF 130
+++ +H CFTC C L+ + + E+K C + +
Sbjct: 18 RDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2. The second LIM
domain of Isl2: Isl is a member of LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Isl proteins are found in the nucleus and act as
transcription factors or cofactors. Isl1 and Isl2 are
the two conserved members of this family. Mouse Isl2 is
expressed in the retinal ganglion cells and the
developing spinal cord where it plays a role in motor
neuron development. Isl2 may be able to bind to the
insulin gene enhancer to promote gene activation. All
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 55
Score = 25.7 bits (56), Expect = 4.5
Identities = 14/30 (46%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 98 WHRECFTCSNCSTS-LAGQRFTSREDKPFC 126
+H ECF CS CS L G F RE + C
Sbjct: 22 YHIECFRCSVCSRQLLPGDEFCLREHELLC 51
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 27.7 bits (62), Expect = 4.7
Identities = 13/57 (22%), Positives = 18/57 (31%), Gaps = 10/57 (17%)
Query: 100 REC---FTCSNCSTSLAGQRFTSREDKPFCADC-FGELFAKRCYSCKKP---ITGIG 149
R+C C NC + L + C C + E + C C G G
Sbjct: 439 RDCGYIAECPNCDSPL---TLHKATGQLRCHYCGYQEPIPQSCPECGSEHLRAVGPG 492
>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 = 25.6 bits (56), Expect = 4.8
Identities = 10/32 (31%), Positives = 16/32 (50%)
Query: 95 NEPWHRECFTCSNCSTSLAGQRFTSREDKPFC 126
+ +H CF CS C+T L+ + S +C
Sbjct: 18 QQIYHNSCFRCSYCNTKLSLGTYASLHGNIYC 49
>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2. The
first LIM domain of Prickle 2: Prickle contains three
C-terminal LIM domains and a N-terminal PET domain.
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts
with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4.
The best characterized is prickle 1 and prickle 2 which
are differentially expressed. While prickle 1 is
expressed in fetal heart and hematological
malignancies, prickle 2 is found in fetal brain, adult
cartilage, pancreatic islet, and some types of timorous
cells. Mutations in prickle 1 have been linked to
progressive myoclonus epilepsy. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 59
Score = 25.7 bits (56), Expect = 4.8
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 8 WHEKCFACVVCKTPIGTKSFIPREQEIYCA 37
WH +CF C VC + + ++ +IYC
Sbjct: 26 WHPQCFVCSVCNELLVDLIYFYQDGKIYCG 55
>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 = 25.5 bits (56), Expect = 5.0
Identities = 12/33 (36%), Positives = 19/33 (57%), Gaps = 2/33 (6%)
Query: 8 WHEKCFACVVCKT--PIGTKSFIPREQEIYCAN 38
+H+ CF C C T + T +F+ + E+YCA
Sbjct: 21 YHKGCFKCRECGTRLSLKTFTFVQGDGEVYCAR 53
>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 = 25.4 bits (56), Expect = 5.1
Identities = 10/29 (34%), Positives = 14/29 (48%)
Query: 98 WHRECFTCSNCSTSLAGQRFTSREDKPFC 126
WH CF CS C L + +D+ +C
Sbjct: 26 WHPACFRCSTCEELLVDLTYCVHDDQIYC 54
Score = 25.4 bits (56), Expect = 5.9
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 161 WHNDCFMCASCQSSLV 176
WH CF C++C+ LV
Sbjct: 26 WHPACFRCSTCEELLV 41
>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle. The first
LIM domain of Prickle: Prickle contains three C-terminal
LIM domains and a N-terminal PET domain. Prickles have
been implicated in roles of regulating tissue polarity
or planar cell polarity (PCP). PCP establishment
requires the conserved Frizzled/Dishevelled PCP pathway.
Prickle interacts with Dishevelled, thereby modulating
Frizzled/Dishevelled activity and PCP signaling. Four
forms of prickles have been identified: prickle 1-4. The
best characterized is prickle 1 and prickle 2 which are
differentially expressed. While prickle 1 is expressed
in fetal heart and hematological malignancies, prickle 2
is found in fetal brain, adult cartilage, pancreatic
islet, and some types of timorous cells. Mutations in
prickle 1 have been linked to progressive myoclonus
epilepsy. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 25.3 bits (56), Expect = 5.3
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 2/41 (4%)
Query: 138 CYSCKKPITGIGGTRFISFEDRH--WHNDCFMCASCQSSLV 176
C C + I+G F S WH CF+C++C+ LV
Sbjct: 1 CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCKELLV 41
Score = 25.3 bits (56), Expect = 6.7
Identities = 7/12 (58%), Positives = 7/12 (58%)
Query: 8 WHEKCFACVVCK 19
WH CF C CK
Sbjct: 26 WHPACFVCSTCK 37
>gnl|CDD|188821 cd09437, LIM3_LPP, The third LIM domain of lipoma preferred partner
(LPP). The third LIM domain of lipoma preferred partner
(LPP): LPP is a member of the zyxin LIM protein family
and contains three LIM zinc-binding domains at the
C-terminal and proline-rich region at the N-terminal.
LPP initially identified as the most frequent
translocation partner of HMGA2 (High Mobility Group A2)
in a subgroup of benign tumors of adipose tissue
(lipomas). It was also shown to be rearranged in a
number of other soft tissues, as well as in a case of
acute monoblastic leukemia. In addition to its
involvement in tumors, LPP was inedited as a smooth
muscle restricted LIM protein that plays an important
role in SMC migration. LPP is localized at sites of cell
adhesion, cell-cell contacts and transiently in the
nucleus. In nucleus, it acts as a coactivator for the
ETS domain transcription factor PEA3. In addition to
PEA3, it interacts with alpha-actinin,vasodilator
stimulated phosphoprotein (VASP), Palladin, and Scrib.
The LIM domains are the main focal adhesion targeting
elements and that the proline- rich region, which
harbors binding sites for alpha-actinin and vasodilator-
stimulated phosphoprotein (VASP), has a weak targeting
capacity. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 68
Score = 25.5 bits (56), Expect = 5.3
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 9/63 (14%)
Query: 138 CYSCKKPITGIGG----TRFISFEDRHWHNDCFMCASC----QSSLVGRGFITDGEDIIC 189
C CK PI G R ++ DR +H C+ C C S GRG + ++C
Sbjct: 1 CCVCKLPIMPEPGQDETVRVVAL-DRSFHVQCYKCEDCGLLLSSEAEGRGCYPLDDHVLC 59
Query: 190 PDC 192
C
Sbjct: 60 KSC 62
>gnl|CDD|188833 cd09449, LIM_Mystique, The LIM domain of Mystique, a subfamily of
ALP LIM domain proteins. The LIM domain of Mystique, a
subfamily of ALP LIM domain proteins: Mystique is the
most recently identified member of the ALP protein
family. It also interacts with alpha-actinin, as other
ALP proteins do. Mystique promotes cell attachment and
migration and suppresses anchorage-independent growth.
The LIM domain of Mystique is required for the
suppression function. Moreover, Mystique functions as an
ubiquitin E3 ligase acting on STAT proteins to cause
their proteosome mediated degradation. As in all LIM
domains, this domain is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 25.2 bits (55), Expect = 5.4
Identities = 16/49 (32%), Positives = 21/49 (42%)
Query: 141 CKKPITGIGGTRFISFEDRHWHNDCFMCASCQSSLVGRGFITDGEDIIC 189
C+K T I E R+ H C+ C C +L RG GE + C
Sbjct: 1 CEKCGTSIVTQAVRIQEGRYRHPGCYTCTDCGLNLKMRGHFWAGEKMFC 49
>gnl|CDD|227914 COG5627, MMS21, DNA repair protein MMS21 [DNA replication,
recombination, and repair].
Length = 275
Score = 27.3 bits (60), Expect = 5.8
Identities = 11/59 (18%), Positives = 21/59 (35%), Gaps = 4/59 (6%)
Query: 1 MEYKTRQWHEKCFACVVCKTPIGTKSFIPREQEIYCANCYEEKFATRC-VKCNKTFFRL 58
+ W + A + KS P E + ++E + RC + N F+ +
Sbjct: 148 LSMDEYIWRAE--ALKAADNIV-MKSPNPEEGLVDKILIHQELLSNRCPITLNPDFYPI 203
>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 = 6.3
Identities = 15/59 (25%), Positives = 28/59 (47%), Gaps = 5/59 (8%)
Query: 136 KRCYSCKKPITGIGGTRFISFEDRHWHNDCFMCASC-QSSLVGRGFITDGEDIICPDCA 193
+C SC+ + G +S + +H CF+C+ C Q G +G++ +C C+
Sbjct: 2 TKCDSCQDFVEG----EVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQKCS 56
Score = 25.0 bits (55), Expect = 7.6
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 6 RQWHEKCFACVVCKTP 21
+ +H KCF C VC+ P
Sbjct: 21 KTYHPKCFVCSVCRQP 36
>gnl|CDD|236244 PRK08329, PRK08329, threonine synthase; Validated.
Length = 347
Score = 26.7 bits (59), Expect = 8.4
Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 1/31 (3%)
Query: 36 CANCYEEKFATRCVKCNKTFFRLREKGTFQS 66
C YEEKF RC C T RE G+F S
Sbjct: 7 CGRTYEEKFKLRC-DCGGTLLVEREYGSFDS 36
>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 = 24.6 bits (54), Expect = 8.6
Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 4/37 (10%)
Query: 7 QWHEKCFACVVCKTPIG---TKSFIPREQEIYCANCY 40
++H +CF+C CK IG + + + R + +YC CY
Sbjct: 19 KFHPECFSCSSCKAFIGDGDSYALVERSK-LYCGVCY 54
>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9. The second LIM
domain of Lhx9: Lhx9 belongs to the LHX protein family,
which features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx9 is highly
homologous to Lhx2. It is expressed in several regions
of the developing mouse brain, the spinal cord, the
pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles exhibit
numerous urogenital defects, such as gonadal agenesis,
infertility, and undetectable levels of testosterone and
estradiol coupled with high FSH levels. Lhx9 null mice
have reduced levels of the Sf1 nuclear receptor that is
required for gonadogenesis, and recent studies have
shown that Lhx9 is able to activate the Sf1/FtzF1 gene.
Lhx9 null mice are phenotypically female, even those
that are genotypically male. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 59
Score = 25.0 bits (54), Expect = 9.0
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 1/30 (3%)
Query: 98 WHRECFTCSNCSTSLA-GQRFTSREDKPFC 126
+H CFTC+ C+ +L G F +++ +C
Sbjct: 26 YHLSCFTCTTCNKTLTTGDHFGMKDNLVYC 55
>gnl|CDD|224299 COG1381, RecO, Recombinational DNA repair protein (RecF pathway)
[DNA replication, recombination, and repair].
Length = 251
Score = 26.5 bits (59), Expect = 9.5
Identities = 8/27 (29%), Positives = 12/27 (44%)
Query: 14 ACVVCKTPIGTKSFIPREQEIYCANCY 40
+C C TP+ F P+ C+ C
Sbjct: 156 SCARCGTPVDPVYFSPKSGGFLCSKCA 182
>gnl|CDD|190632 pfam03431, RNA_replicase_B, RNA replicase, beta-chain. This family
is of Leviviridae RNA replicases. The replicase is also
known as RNA dependent RNA polymerase.
Length = 540
Score = 26.7 bits (59), Expect = 9.6
Identities = 9/15 (60%), Positives = 10/15 (66%)
Query: 184 GEDIICPDCAKAKLM 198
G+DII P CA LM
Sbjct: 332 GDDIIVPSCAVPPLM 346
>gnl|CDD|235202 PRK04023, PRK04023, DNA polymerase II large subunit; Validated.
Length = 1121
Score = 26.8 bits (60), Expect = 9.7
Identities = 7/27 (25%), Positives = 9/27 (33%)
Query: 46 TRCVKCNKTFFRLREKGTFQSHSGRIN 72
RC KC + R G G +
Sbjct: 1038 FRCTKCGAKYRRPPLSGKCPKCGGNLI 1064
>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b. The second
LIM domain of Lhx3b. Lhx3b is a member of LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene
is expressed in the ventral spinal cord, the pons, the
medulla oblongata, and the pineal gland of the
developing nervous system during mouse embryogenesis,
and transcripts are found in the emergent pituitary
gland. Lhx3 functions in concert with other
transcription factors to specify interneuron and motor
neuron fates during development. Lhx3 proteins have
been demonstrated to directly bind to the promoters of
several pituitary hormone gene promoters. The Lhx3 gene
encodes two isoforms, LHX3a and LHX3b that differ in
their amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes
containing a high-affinity Lhx3 binding site more
effectively than the hLhx3b isoform. In addition,
hLhx3a induce transcription of the TSHbeta-subunit gene
by acting on pituitary POU domain factor, Pit-1, while
hLhx3b does not. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 57
Score = 24.6 bits (53), Expect = 10.0
Identities = 9/17 (52%), Positives = 12/17 (70%)
Query: 8 WHEKCFACVVCKTPIGT 24
+H CFAC+VCK + T
Sbjct: 23 YHLHCFACIVCKRQLAT 39
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
0.328 0.140 0.482
Gapped
Lambda K H
0.267 0.0654 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,557,166
Number of extensions: 823394
Number of successful extensions: 1685
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1635
Number of HSP's successfully gapped: 479
Length of query: 198
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 106
Effective length of database: 6,857,034
Effective search space: 726845604
Effective search space used: 726845604
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 56 (25.5 bits)