RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10533
(594 letters)
>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 = 120 bits (304), Expect = 3e-33
Identities = 50/59 (84%), Positives = 55/59 (93%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFHVLFA 66
C RC EGFEP+EKIVNSNGEL+H+QCFVCAQCF+PFP G+FYEFEGRKYCEHDF VLFA
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
Score = 59.3 bits (144), Expect = 2e-11
Identities = 21/31 (67%), Positives = 25/31 (80%)
Query: 122 TLTGGAWHQQCFVCAQCFRPFPGGIFYEFEG 152
G +H+QCFVCAQCF+PFP G+FYEFEG
Sbjct: 16 NSNGELYHEQCFVCAQCFQPFPDGLFYEFEG 46
Score = 45.8 bits (109), Expect = 1e-06
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 2/58 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 335
C CR E E++V + G+ +H + FVCA+C +PF YE +G YCE + LF
Sbjct: 1 CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLF 58
Score = 38.9 bits (91), Expect = 3e-04
Identities = 17/40 (42%), Positives = 24/40 (60%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 449
G+ +H + FVCA+C +PF YE +G YCE + LF
Sbjct: 19 GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLF 58
Score = 26.9 bits (60), Expect = 4.5
Identities = 11/38 (28%), Positives = 15/38 (39%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHECNAQAKA 204
+H +CF C C + D F +GR C A
Sbjct: 22 YHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDFQVLFA 59
>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH. The
fourth LIM domain of protein PINCH: PINCH plays a
pivotal role in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
The PINCH LIM4 domain recognizes the third SH3 domain of
another adaptor protein, Nck2. This step is an important
component of integrin signaling event. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the assem
bly of multimeric protein complexes.
Length = 54
Score = 108 bits (271), Expect = 8e-29
Identities = 52/54 (96%), Positives = 53/54 (98%)
Query: 278 PICGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
PICGACRRPIE RVVTALGKHWHVEHFVCA+CEKPFLGHRHYEKKGLAYCETHY
Sbjct: 1 PICGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 82.4 bits (204), Expect = 1e-19
Identities = 36/40 (90%), Positives = 38/40 (95%)
Query: 406 CSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
+ LGKHWHVEHFVCA+CEKPFLGHRHYEKKGLAYCETHY
Sbjct: 15 VTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 45.8 bits (109), Expect = 9e-07
Identities = 21/55 (38%), Positives = 30/55 (54%), Gaps = 2/55 (3%)
Query: 7 YCSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C C E ++V + G+ WH + FVCA+C +PF G YE +G YCE +
Sbjct: 2 ICGACRR--PIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54
Score = 37.3 bits (87), Expect = 0.001
Identities = 15/18 (83%), Positives = 15/18 (83%)
Query: 532 FGLRHYEKNGLAYCETHY 549
G RHYEK GLAYCETHY
Sbjct: 37 LGHRHYEKKGLAYCETHY 54
Score = 33.5 bits (77), Expect = 0.020
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 13/62 (20%)
Query: 134 VCAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRA 193
+C C RP + GRV+ A+ +WH + F C C K +G A
Sbjct: 2 ICGACRRP-------------IEGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLA 48
Query: 194 LC 195
C
Sbjct: 49 YC 50
Score = 31.2 bits (71), Expect = 0.12
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEG 152
G WH + FVCA+C +PF G YE +G
Sbjct: 19 GKHWHVEHFVCAKCEKPFLGHRHYEKKG 46
>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 = 92.4 bits (230), Expect = 3e-23
Identities = 38/48 (79%), Positives = 43/48 (89%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHECN 199
GEFVIGRVIKAMN NWHP CFRCE C+KELAD+GF+++ GRALCH CN
Sbjct: 5 GEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPCN 52
Score = 26.5 bits (59), Expect = 5.0
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKP 312
CG C + RV+ A+ +WH + F C C K
Sbjct: 1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKE 33
>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 = 82.8 bits (205), Expect = 6e-20
Identities = 34/61 (55%), Positives = 43/61 (70%), Gaps = 10/61 (16%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTANDMNELYCLRC 271
C KCH +I+++ LKF+G+ YHPYHFNC +CG EL +DARE+K ELYCLRC
Sbjct: 1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKELTADARELK----------GELYCLRC 50
Query: 272 H 272
H
Sbjct: 51 H 51
Score = 28.5 bits (64), Expect = 1.2
Identities = 19/48 (39%), Positives = 22/48 (45%), Gaps = 1/48 (2%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C IEE+ + G +H HF CA C K L E KG YC
Sbjct: 1 CQKCHAIIEEQHLKFKGDPYHPYHFNCANCGKE-LTADARELKGELYC 47
>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 = 64.7 bits (158), Expect = 2e-13
Identities = 28/53 (52%), Positives = 34/53 (64%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
C AC++PI +VVTALGK WH EHFVCA C+ +E+ G YCE YH
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53
Score = 49.6 bits (119), Expect = 3e-08
Identities = 25/67 (37%), Positives = 30/67 (44%), Gaps = 14/67 (20%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C C + I G + TAL GK WH EHFVCA C+ +E+ G
Sbjct: 1 CAACKKPIVGQVVTAL--------------GKTWHPEHFVCAECKTELGTKNFFERDGQP 46
Query: 440 YCETHYH 446
YCE YH
Sbjct: 47 YCEKDYH 53
Score = 41.2 bits (97), Expect = 3e-05
Identities = 14/44 (31%), Positives = 22/44 (50%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
++G+V+ A+ WHP+ F C C EL F G+ C +
Sbjct: 8 IVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKD 51
Score = 40.8 bits (96), Expect = 5e-05
Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
C+ C + ++V + G+ WH + FVCA+C F+E +G+ YCE D+H
Sbjct: 1 CAACKK--PIVGQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53
Score = 31.1 bits (71), Expect = 0.12
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNS 247
C C I + + G+ +HP HF C C TEL +
Sbjct: 1 CAACKKPIVGQVVTALGKTWHPEHFVCAECKTELGT 36
>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 = 64.3 bits (157), Expect = 3e-13
Identities = 28/53 (52%), Positives = 34/53 (64%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
CG C +PI E ++AL WH E FVC C KPF+ +E +GL YCETHYH
Sbjct: 1 CGGCNKPILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53
Score = 52.0 bits (125), Expect = 5e-09
Identities = 18/37 (48%), Positives = 23/37 (62%)
Query: 26 GELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
WH +CFVC +C +PF G F+E EG YCE +H
Sbjct: 17 NTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53
Score = 48.1 bits (115), Expect = 1e-07
Identities = 22/40 (55%), Positives = 25/40 (62%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 446
S L WH E FVC C KPF+ +E +GL YCETHYH
Sbjct: 14 SALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53
Score = 42.3 bits (100), Expect = 1e-05
Identities = 14/28 (50%), Positives = 18/28 (64%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEG 152
WH +CFVC +C +PF G F+E EG
Sbjct: 17 NTQWHPECFVCRECHKPFINGSFFEHEG 44
Score = 36.2 bits (84), Expect = 0.002
Identities = 14/41 (34%), Positives = 20/41 (48%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
++ I A+N WHP+CF C C K + F +G C
Sbjct: 8 ILENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYC 48
>gnl|CDD|215907 pfam00412, LIM, LIM domain. This family represents two copies of
the LIM structural domain.
Length = 58
Score = 63.9 bits (156), Expect = 3e-13
Identities = 22/58 (37%), Positives = 35/58 (60%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFHVLF 65
C+ C + E + + G++WH +CF CA C +P G F+E +G+ YC+HD+ LF
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 58.9 bits (143), Expect = 2e-11
Identities = 26/58 (44%), Positives = 32/58 (55%), Gaps = 2/58 (3%)
Query: 280 CGACRRPIEERVVT--ALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 335
C C +PI +R + ALGK WH E F CA C KP +EK G YC+ Y +LF
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 48.5 bits (116), Expect = 9e-08
Identities = 20/41 (48%), Positives = 23/41 (56%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 449
LGK WH E F CA C KP +EK G YC+ Y +LF
Sbjct: 18 LGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58
Score = 38.9 bits (91), Expect = 3e-04
Identities = 15/41 (36%), Positives = 19/41 (46%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
V +A+ WHP+CFRC C K L F G+ C
Sbjct: 13 LVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHD 53
Score = 36.6 bits (85), Expect = 0.002
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 127 AWHQQCFVCAQCFRPFPGGIFYEFEGEFV 155
WH +CF CA C +P G F+E +G+
Sbjct: 21 VWHPECFRCAVCGKPLGPGDFFEKDGKLY 49
Score = 36.6 bits (85), Expect = 0.002
Identities = 20/66 (30%), Positives = 27/66 (40%), Gaps = 11/66 (16%)
Query: 212 CHKCHGLIDDKPL--KFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTANDMNELYCL 269
C C I D+ L + G+V+HP F C CG L PG +LYC
Sbjct: 1 CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLG---------PGDFFEKDGKLYCK 51
Query: 270 RCHDKM 275
+ K+
Sbjct: 52 HDYFKL 57
>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 = 61.6 bits (150), Expect = 2e-12
Identities = 26/52 (50%), Positives = 30/52 (57%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C PI ++ VTAL K WH EHF CA+C KPF +EK G YC Y
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 45.5 bits (108), Expect = 1e-06
Identities = 25/66 (37%), Positives = 27/66 (40%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C CN I TAL K WH EHF CA+C KPF +EK G
Sbjct: 1 CAYCNGPILDKCVTAL--------------DKTWHPEHFFCAQCGKPFGDEGFHEKDGKP 46
Query: 440 YCETHY 445
YC Y
Sbjct: 47 YCREDY 52
Score = 40.8 bits (96), Expect = 5e-05
Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 19 EKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
+K V + + WH + F CAQC +PF F+E +G+ YC D+
Sbjct: 10 DKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52
Score = 36.6 bits (85), Expect = 0.001
Identities = 14/43 (32%), Positives = 22/43 (51%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
++ + + A++ WHP+ F C C K D GF G+ C E
Sbjct: 8 ILDKCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCRE 50
Score = 29.7 bits (67), Expect = 0.38
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 122 TLTGGAWHQQCFVCAQCFRPFPGGIFYEFEGE 153
T WH + F CAQC +PF F+E +G+
Sbjct: 14 TALDKTWHPEHFFCAQCGKPFGDEGFHEKDGK 45
Score = 29.3 bits (66), Expect = 0.59
Identities = 13/31 (41%), Positives = 17/31 (54%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCG 242
C C+G I DK + + +HP HF C CG
Sbjct: 1 CAYCNGPILDKCVTALDKTWHPEHFFCAQCG 31
>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 = 60.3 bits (146), Expect = 6e-12
Identities = 27/53 (50%), Positives = 35/53 (66%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
C +C++PI +VVTALG+ WH EHFVC +C K +E+ G AYCE YH
Sbjct: 3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55
Score = 44.1 bits (104), Expect = 3e-06
Identities = 25/67 (37%), Positives = 31/67 (46%), Gaps = 14/67 (20%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C C + I G + TAL G+ WH EHFVC +C K +E+ G A
Sbjct: 3 CASCQKPIAGQVVTAL--------------GQTWHPEHFVCCQCGKELGSRPFFERNGQA 48
Query: 440 YCETHYH 446
YCE YH
Sbjct: 49 YCEEDYH 55
Score = 39.9 bits (93), Expect = 1e-04
Identities = 21/63 (33%), Positives = 28/63 (44%), Gaps = 13/63 (20%)
Query: 135 CAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRAL 194
CA C +P + G+V+ A+ WHP+ F C C KEL F G+A
Sbjct: 3 CASCQKP-------------IAGQVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAY 49
Query: 195 CHE 197
C E
Sbjct: 50 CEE 52
Score = 39.9 bits (93), Expect = 1e-04
Identities = 17/43 (39%), Positives = 26/43 (60%)
Query: 20 KIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
++V + G+ WH + FVC QC + F+E G+ YCE D+H
Sbjct: 13 QVVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDYH 55
Score = 29.8 bits (67), Expect = 0.44
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 211 MCHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNS 247
C C I + + G+ +HP HF C CG EL S
Sbjct: 2 DCASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGS 38
>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 = 59.7 bits (145), Expect = 1e-11
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHD 60
C+ C + E+++ + G++WH +CF CA C +P G F+E +G+ YC+
Sbjct: 2 CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 56.2 bits (136), Expect = 2e-10
Identities = 26/54 (48%), Positives = 30/54 (55%), Gaps = 2/54 (3%)
Query: 279 ICGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 330
C C +PI ERV+ ALGK WH E F CA C KP G +EK G YC+
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54
Score = 45.8 bits (109), Expect = 7e-07
Identities = 22/65 (33%), Positives = 25/65 (38%), Gaps = 12/65 (18%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C C + I G LGK WH E F CA C KP G +EK G
Sbjct: 2 CAGCGKPIYGT------------ERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKL 49
Query: 440 YCETH 444
YC+
Sbjct: 50 YCKDC 54
Score = 43.5 bits (103), Expect = 5e-06
Identities = 21/65 (32%), Positives = 30/65 (46%), Gaps = 11/65 (16%)
Query: 134 VCAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRA 193
CA C +P G RV++A+ WHP+CF+C C K L+ F G+
Sbjct: 1 KCAGCGKPIYGT-----------ERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKL 49
Query: 194 LCHEC 198
C +C
Sbjct: 50 YCKDC 54
Score = 35.4 bits (82), Expect = 0.004
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 11/63 (17%)
Query: 211 MCHKCHGLIDD--KPLKFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTANDMNELYC 268
C C I + L+ G+V+HP F C +CG L+ D +LYC
Sbjct: 1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGD---------TFFEKDGKLYC 51
Query: 269 LRC 271
C
Sbjct: 52 KDC 54
Score = 35.1 bits (81), Expect = 0.005
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEGEF 154
G WH +CF CA C +P G F+E +G+
Sbjct: 20 GKVWHPECFKCATCGKPLSGDTFFEKDGKL 49
>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 = 59.6 bits (144), Expect = 1e-11
Identities = 27/54 (50%), Positives = 36/54 (66%)
Query: 279 ICGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
+CGAC++PI +VVTA+GK WH EHFVC C++ +E+ G YCE YH
Sbjct: 1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54
Score = 40.4 bits (94), Expect = 7e-05
Identities = 23/68 (33%), Positives = 31/68 (45%), Gaps = 14/68 (20%)
Query: 379 LCFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGL 438
+C C + I G + TA+ GK WH EHFVC C++ +E+ G
Sbjct: 1 VCGACKKPIAGQVVTAM--------------GKTWHPEHFVCTHCQEEIGSRNFFERDGQ 46
Query: 439 AYCETHYH 446
YCE YH
Sbjct: 47 PYCEKDYH 54
Score = 37.3 bits (86), Expect = 9e-04
Identities = 16/43 (37%), Positives = 25/43 (58%)
Query: 20 KIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
++V + G+ WH + FVC C F+E +G+ YCE D+H
Sbjct: 12 QVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQPYCEKDYH 54
Score = 36.5 bits (84), Expect = 0.002
Identities = 19/64 (29%), Positives = 28/64 (43%), Gaps = 13/64 (20%)
Query: 134 VCAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRA 193
VC C +P + G+V+ AM WHP+ F C HC +E+ F G+
Sbjct: 1 VCGACKKP-------------IAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNFFERDGQP 47
Query: 194 LCHE 197
C +
Sbjct: 48 YCEK 51
Score = 28.1 bits (62), Expect = 1.9
Identities = 13/37 (35%), Positives = 19/37 (51%)
Query: 211 MCHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNS 247
+C C I + + G+ +HP HF CT C E+ S
Sbjct: 1 VCGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGS 37
>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 = 57.7 bits (140), Expect = 4e-11
Identities = 27/53 (50%), Positives = 31/53 (58%), Gaps = 1/53 (1%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C +PIE R ++ ALGK WH E F C+ C KP G YEK G YCE Y
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 52.3 bits (126), Expect = 4e-09
Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+ C + E E ++ + G+ WH +CF C+ C +P G FYE +G+ YCE +
Sbjct: 1 CAGCGKPIEGRE-LLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53
Score = 46.5 bits (111), Expect = 4e-07
Identities = 24/66 (36%), Positives = 26/66 (39%), Gaps = 13/66 (19%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C C + I G LGK WH E F C+ C KP G YEK G
Sbjct: 1 CAGCGKPIEGR-------------ELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKP 47
Query: 440 YCETHY 445
YCE Y
Sbjct: 48 YCEKCY 53
Score = 44.6 bits (106), Expect = 2e-06
Identities = 17/48 (35%), Positives = 26/48 (54%), Gaps = 1/48 (2%)
Query: 152 GEFVIGRVI-KAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
G+ + GR + +A+ WHP+CF+C C K L F G+ C +C
Sbjct: 5 GKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKC 52
Score = 36.1 bits (84), Expect = 0.002
Identities = 17/62 (27%), Positives = 27/62 (43%), Gaps = 10/62 (16%)
Query: 212 CHKCHGLIDDKPL-KFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTANDMNELYCLR 270
C C I+ + L + G+ +HP F C+ CG L D + D + YC +
Sbjct: 1 CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGD--------SFYEKD-GKPYCEK 51
Query: 271 CH 272
C+
Sbjct: 52 CY 53
Score = 34.6 bits (80), Expect = 0.007
Identities = 14/39 (35%), Positives = 20/39 (51%)
Query: 116 RGEDRQTLTGGAWHQQCFVCAQCFRPFPGGIFYEFEGEF 154
G + G WH +CF C+ C +P G FYE +G+
Sbjct: 9 EGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKP 47
>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 = 53.7 bits (129), Expect = 2e-09
Identities = 25/53 (47%), Positives = 29/53 (54%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
CG C R I E ++AL WH E FVC C PF+ +E G YCE HYH
Sbjct: 1 CGGCARAILENYISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53
Score = 50.2 bits (120), Expect = 2e-08
Identities = 19/35 (54%), Positives = 25/35 (71%)
Query: 28 LWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
LWH +CFVC +CF PF G F+E +G+ YCE +H
Sbjct: 19 LWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53
Score = 41.0 bits (96), Expect = 4e-05
Identities = 19/40 (47%), Positives = 21/40 (52%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 446
S L WH E FVC C PF+ +E G YCE HYH
Sbjct: 14 SALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYCEAHYH 53
Score = 38.7 bits (90), Expect = 3e-04
Identities = 14/26 (53%), Positives = 19/26 (73%)
Query: 128 WHQQCFVCAQCFRPFPGGIFYEFEGE 153
WH +CFVC +CF PF G F+E +G+
Sbjct: 20 WHPECFVCRECFTPFVNGSFFEHDGQ 45
Score = 33.3 bits (76), Expect = 0.020
Identities = 13/36 (36%), Positives = 17/36 (47%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
I A+N WHP+CF C C + F G+ C
Sbjct: 13 ISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPYC 48
>gnl|CDD|188721 cd09335, LIM5_PINCH, The fifth LIM domain of protein PINCH. The
fifth LIM domain of protein PINCH: PINCH plays pivotal
roles in the assembly of focal adhesions (FAs),
regulating diverse functions in cell adhesion, growth,
and differentiation through LIM-mediated protein-protein
interactions. PINCH comprises an array of five LIM
domains that interact with integrin-linked kinase (ILK),
Nck2 (also called Nckbeta or Grb4) and other interaction
partners. These interactions are essential for
triggering the FA assembly and for relaying diverse
mechanical and biochemical signals between
Cell-extracellular matrix and the actin cytoskeleton.
LIM domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 54
Score = 50.0 bits (120), Expect = 3e-08
Identities = 19/28 (67%), Positives = 23/28 (82%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACS 407
C+ CNQVI GD+ +ALNK WCV HF+CS
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCS 28
Score = 36.2 bits (84), Expect = 0.002
Identities = 15/34 (44%), Positives = 20/34 (58%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPF 313
C C + IE VV+AL K W V+HF C+ C+
Sbjct: 1 CYHCNQVIEGDVVSALNKTWCVDHFSCSFCDTKL 34
Score = 26.9 bits (60), Expect = 4.7
Identities = 12/43 (27%), Positives = 18/43 (41%), Gaps = 1/43 (2%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELA-DLGFIRSQGRALCHEC 198
G V+ A+N W F C C +L F + +C +C
Sbjct: 10 GDVVSALNKTWCVDHFSCSFCDTKLTLKSKFYEFDMKPVCKKC 52
>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 = 49.4 bits (118), Expect = 5e-08
Identities = 23/53 (43%), Positives = 29/53 (54%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
C C RP++E ++A WH E FVC+ C KPF +E G CE HYH
Sbjct: 1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53
Score = 49.4 bits (118), Expect = 5e-08
Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 2/55 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
CS C + E +++ +WH +CFVC+ C +PF G F+E +GR CE +H
Sbjct: 1 CSGCGRPVK--ENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53
Score = 39.0 bits (91), Expect = 2e-04
Identities = 14/27 (51%), Positives = 19/27 (70%)
Query: 126 GAWHQQCFVCAQCFRPFPGGIFYEFEG 152
G WH +CFVC+ C +PF G F+E +G
Sbjct: 18 GVWHPECFVCSDCLKPFTDGSFFELDG 44
Score = 36.3 bits (84), Expect = 0.002
Identities = 18/44 (40%), Positives = 20/44 (45%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
G V + A N WHP+CF C C K D F GR LC
Sbjct: 5 GRPVKENYLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48
Score = 36.3 bits (84), Expect = 0.002
Identities = 17/34 (50%), Positives = 19/34 (55%)
Query: 413 WHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 446
WH E FVC+ C KPF +E G CE HYH
Sbjct: 20 WHPECFVCSDCLKPFTDGSFFELDGRPLCELHYH 53
>gnl|CDD|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin. The
second LIM domain of paxillin: Paxillin is an adaptor
protein, which recruits key components of the
signal-transduction machinery to specific sub-cellular
locations to respond to environmental changes rapidly.
The C-terminal region of paxillin contains four LIM
domains which target paxillin to focal adhesions,
presumably through a direct association with the
cytoplasmic tail of beta-integrin. The N-terminal of
paxillin is leucine-rich LD-motifs. Paxillin is found at
the interface between the plasma membrane and the actin
cytoskeleton. The binding partners of paxillin are
diverse and include protein tyrosine kinases, such as
Src and FAK, structural proteins, such as vinculin and
actopaxin, and regulators of actin organization.
Paxillin recruits these proteins to their function sites
to control the dynamic changes in cell adhesion,
cytoskeletal reorganization and gene expression. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 52
Score = 49.2 bits (117), Expect = 6e-08
Identities = 25/52 (48%), Positives = 30/52 (57%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C PI ++VVTAL + WH EHF CA+C F +EK G AYC Y
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
Score = 36.5 bits (84), Expect = 0.002
Identities = 23/66 (34%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C+ CN I + TAL++ W H EHF CA+C F +EK G A
Sbjct: 1 CYYCNGPILDKVVTALDRTW--------------HPEHFFCAQCGAFFGPEGFHEKDGKA 46
Query: 440 YCETHY 445
YC Y
Sbjct: 47 YCRKDY 52
Score = 34.2 bits (78), Expect = 0.013
Identities = 16/43 (37%), Positives = 24/43 (55%)
Query: 19 EKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
+K+V + WH + F CAQC F F+E +G+ YC D+
Sbjct: 10 DKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52
Score = 32.2 bits (73), Expect = 0.050
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
++ +V+ A++ WHP+ F C C GF G+A C +
Sbjct: 8 ILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRK 50
Score = 29.5 bits (66), Expect = 0.55
Identities = 16/51 (31%), Positives = 21/51 (41%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTAND 262
C+ C+G I DK + +HP HF C CG + K Y D
Sbjct: 1 CYYCNGPILDKVVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKD 51
>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 = 48.3 bits (115), Expect = 3e-07
Identities = 20/54 (37%), Positives = 26/54 (48%)
Query: 5 NMYCSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
N C C + + V + G L+H CF C QC + G FY EG+ YCE
Sbjct: 31 NELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCE 84
Score = 47.2 bits (112), Expect = 7e-07
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 280 CGACRRPI--EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
CG C +P+ + V ALG +HV F C +CE+ G + Y +G YCE Y
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
Score = 35.6 bits (82), Expect = 0.008
Identities = 16/41 (39%), Positives = 21/41 (51%)
Query: 405 ACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
A LG +HV F C +CE+ G + Y +G YCE Y
Sbjct: 47 AVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEECY 87
Score = 31.7 bits (72), Expect = 0.17
Identities = 12/40 (30%), Positives = 20/40 (50%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
++A+ +H CF C C ++L F +G+ C EC
Sbjct: 47 AVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEEC 86
Score = 27.9 bits (62), Expect = 3.5
Identities = 11/25 (44%), Positives = 13/25 (52%)
Query: 128 WHQQCFVCAQCFRPFPGGIFYEFEG 152
+H CF C QC + G FY EG
Sbjct: 55 FHVTCFTCHQCEQQLQGQQFYSLEG 79
>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 = 45.7 bits (109), Expect = 8e-07
Identities = 15/50 (30%), Positives = 25/50 (50%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C + P K + G+ WH++CF C++C +P F + + YC
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYC 50
Score = 33.4 bits (77), Expect = 0.018
Identities = 19/65 (29%), Positives = 25/65 (38%), Gaps = 13/65 (20%)
Query: 135 CAQCFRPF-PGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRA 193
C C + PG E++G+F WH KCF C C K + FI +
Sbjct: 1 CKACGKAIMPGSKKMEYKGKF------------WHEKCFTCSECKKPIGTKSFIPKDDKI 48
Query: 194 LCHEC 198
C C
Sbjct: 49 YCVPC 53
Score = 28.8 bits (65), Expect = 1.1
Identities = 17/54 (31%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C AC + I + + GK WH + F C+ C+KP K YC Y
Sbjct: 1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
Score = 26.9 bits (60), Expect = 5.1
Identities = 10/39 (25%), Positives = 18/39 (46%)
Query: 117 GEDRQTLTGGAWHQQCFVCAQCFRPFPGGIFYEFEGEFV 155
G + G WH++CF C++C +P F + +
Sbjct: 11 GSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIY 49
Score = 26.1 bits (58), Expect = 8.9
Identities = 13/36 (36%), Positives = 16/36 (44%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
GK WH + F C+ C+KP K YC Y
Sbjct: 19 GKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54
>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 = 45.6 bits (108), Expect = 9e-07
Identities = 19/48 (39%), Positives = 26/48 (54%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C PI + V+TA+ + WH EHF C+ C + F E+ G YC
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYC 48
Score = 39.0 bits (91), Expect = 2e-04
Identities = 15/43 (34%), Positives = 23/43 (53%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
++ V+ AM+ WHP+ F C HC + D GF+ G+ C
Sbjct: 8 ILQNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRR 50
Score = 31.3 bits (71), Expect = 0.11
Identities = 13/43 (30%), Positives = 22/43 (51%)
Query: 19 EKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
+ ++ + + WH + F C+ C F F E +G+ YC DF
Sbjct: 10 QNVLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52
Score = 30.2 bits (68), Expect = 0.29
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
+ + + WH EHF C+ C + F E+ G YC
Sbjct: 14 TAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYC 48
Score = 28.2 bits (63), Expect = 1.3
Identities = 12/31 (38%), Positives = 15/31 (48%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCG 242
C C G I L + +HP HF C+ CG
Sbjct: 1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCG 31
>gnl|CDD|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and
RhoGap domain containing protein. The second LIM domain
of Lrg1p, a LIM and RhoGap domain containing protein:
The members of this family contain three tandem repeats
of LIM domains and a Rho-type GTPase activating protein
(RhoGap) domain. Lrg1p is a Rho1 GTPase-activating
protein required for efficient cell fusion in yeast.
Lrg1p-GAP domain strongly and specifically stimulates
the GTPase activity of Rho1p, a regulator of beta
(1-3)-glucan synthase in vitro. The LIM domain is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 45.4 bits (108), Expect = 1e-06
Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHR-HYEKKGLAYCETHY 331
C C + +TALG+ +HVEHF C+ C F + +YE +G YC HY
Sbjct: 1 CFKCGGALRGSYITALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
Score = 37.7 bits (88), Expect = 6e-04
Identities = 23/67 (34%), Positives = 30/67 (44%), Gaps = 15/67 (22%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHR-HYEKKGL 438
CF C + G TAL G+ +HVEHF C+ C F + +YE +G
Sbjct: 1 CFKCGGALRGSYITAL--------------GRKYHVEHFTCSVCPTVFGPNDSYYEHEGK 46
Query: 439 AYCETHY 445
YC HY
Sbjct: 47 IYCHYHY 53
Score = 27.7 bits (62), Expect = 2.5
Identities = 12/34 (35%), Positives = 19/34 (55%), Gaps = 1/34 (2%)
Query: 29 WHQQCFVCAQCFRPF-PGGIFYEFEGRKYCEHDF 61
+H + F C+ C F P +YE EG+ YC + +
Sbjct: 20 YHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53
>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 = 44.6 bits (105), Expect = 2e-06
Identities = 22/52 (42%), Positives = 28/52 (53%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
CG C+R I V+ AL + WHV FVC C P + + + G YCET Y
Sbjct: 1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 41.9 bits (98), Expect = 2e-05
Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C RC E ++N+ + WH CFVC C P +F+ +G YCE D+
Sbjct: 1 CGRCQRKILGE--VINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 32.7 bits (74), Expect = 0.039
Identities = 15/39 (38%), Positives = 20/39 (51%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
+ L + WHV FVC C P + + + G YCET Y
Sbjct: 14 NALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52
Score = 29.2 bits (65), Expect = 0.73
Identities = 13/41 (31%), Positives = 18/41 (43%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
++G VI A+ WH CF C C + + F G C
Sbjct: 8 ILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYC 48
Score = 28.8 bits (64), Expect = 0.99
Identities = 11/26 (42%), Positives = 14/26 (53%)
Query: 128 WHQQCFVCAQCFRPFPGGIFYEFEGE 153
WH CFVC C P +F+ +GE
Sbjct: 20 WHVSCFVCVACHNPIRNNVFHLEDGE 45
>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 = 44.2 bits (105), Expect = 4e-06
Identities = 22/60 (36%), Positives = 32/60 (53%), Gaps = 7/60 (11%)
Query: 8 CSRCNEGFEPEEK-IVNSNGEL---WHQQCFVCAQCFRPFPGGI-FYEFEGRKYCEHDFH 62
C +C E E K I + +GEL WH++CFVC C PF + Y + + YC+ +H
Sbjct: 1 CRKCGL--EIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHYH 58
Score = 33.8 bits (78), Expect = 0.019
Identities = 20/58 (34%), Positives = 24/58 (41%), Gaps = 5/58 (8%)
Query: 280 CGACRRPIEERVVT----ALGKHWHVEHFVCARCEKPFLGHRH-YEKKGLAYCETHYH 332
C C IE + ++ L WH E FVC C PF Y YC+ HYH
Sbjct: 1 CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHYH 58
Score = 30.7 bits (70), Expect = 0.20
Identities = 15/35 (42%), Positives = 16/35 (45%), Gaps = 1/35 (2%)
Query: 413 WHVEHFVCARCEKPFLGHRH-YEKKGLAYCETHYH 446
WH E FVC C PF Y YC+ HYH
Sbjct: 24 WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHYH 58
Score = 29.9 bits (68), Expect = 0.38
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 1/29 (3%)
Query: 126 GAWHQQCFVCAQCFRPFPGGI-FYEFEGE 153
G WH++CFVC C PF + Y + +
Sbjct: 22 GQWHRECFVCTTCGCPFQFSVPCYVLDDK 50
>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 = 43.6 bits (103), Expect = 4e-06
Identities = 23/52 (44%), Positives = 31/52 (59%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
CG+C PI R ++ALG+ +H EHFVCA C +P E+ G YC T +
Sbjct: 1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
Score = 34.7 bits (80), Expect = 0.008
Identities = 17/50 (34%), Positives = 24/50 (48%), Gaps = 2/50 (4%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C + +++ G +H + FVCA C RP G F E G+ YC
Sbjct: 1 CGSCGLPITG--RCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYC 48
Score = 30.5 bits (69), Expect = 0.21
Identities = 17/39 (43%), Positives = 22/39 (56%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
S LG+ +H EHFVCA C +P E+ G YC T +
Sbjct: 14 SALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52
Score = 30.1 bits (68), Expect = 0.29
Identities = 15/47 (31%), Positives = 21/47 (44%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
G + GR I A+ +HP+ F C C + L F G+ C C
Sbjct: 5 GLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTC 51
>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 = 43.1 bits (102), Expect = 8e-06
Identities = 19/52 (36%), Positives = 24/52 (46%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + I + ALG+ WH E F C+ C E+KG YCE Y
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52
Score = 40.0 bits (94), Expect = 8e-05
Identities = 16/44 (36%), Positives = 25/44 (56%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
+ G + A+ +WHP+ F C HC LA++GF+ +G C C
Sbjct: 8 IRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELC 51
Score = 33.5 bits (77), Expect = 0.017
Identities = 24/66 (36%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C CNQVI G AL ++W F CS H C+ E F+ E+KG
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCS---------HCHCSLAEIGFV-----EEKGSL 46
Query: 440 YCETHY 445
YCE Y
Sbjct: 47 YCELCY 52
Score = 30.8 bits (70), Expect = 0.15
Identities = 15/52 (28%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEH 59
C+ CN+ + + G WH + F C+ C F E +G YCE
Sbjct: 1 CAHCNQ--VIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCEL 50
Score = 26.9 bits (60), Expect = 4.1
Identities = 11/34 (32%), Positives = 15/34 (44%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTEL 245
C C+ +I L G +HP F C+ C L
Sbjct: 1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSL 34
>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 = 43.2 bits (102), Expect = 8e-06
Identities = 19/54 (35%), Positives = 26/54 (48%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C +C +G + + G L+H CF C C R G FY G+ YCE D+
Sbjct: 1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
Score = 27.0 bits (60), Expect = 3.6
Identities = 14/41 (34%), Positives = 17/41 (41%)
Query: 405 ACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
AC +G +H F C C + G Y G YCE Y
Sbjct: 14 ACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCEEDY 54
>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 = 42.8 bits (101), Expect = 1e-05
Identities = 21/51 (41%), Positives = 28/51 (54%), Gaps = 2/51 (3%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCA--RCEKPFLGHRHYEKKGLAYCE 328
C +C + I +TALGK W +HF+CA C +P E+KG YCE
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCE 51
Score = 35.9 bits (83), Expect = 0.003
Identities = 24/63 (38%), Positives = 27/63 (42%), Gaps = 12/63 (19%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C CNQ I G TAL K WC HF C+ A C +P E+KG
Sbjct: 1 CESCNQQIRGPFITALGKIWCPDHFICAN------------ASCRRPLQDIGFVEEKGQL 48
Query: 440 YCE 442
YCE
Sbjct: 49 YCE 51
Score = 32.8 bits (75), Expect = 0.034
Identities = 15/44 (34%), Positives = 21/44 (47%), Gaps = 2/44 (4%)
Query: 157 GRVIKAMNANWHPKCFRC--EHCSKELADLGFIRSQGRALCHEC 198
G I A+ W P F C C + L D+GF+ +G+ C C
Sbjct: 10 GPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYC 53
Score = 31.3 bits (71), Expect = 0.13
Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 4/56 (7%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCA--QCFRPFPGGIFYEFEGRKYCEHDF 61
C CN+ + + + G++W F+CA C RP F E +G+ YCE+ F
Sbjct: 1 CESCNQ--QIRGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYCF 54
>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like
family. The second LIM domain of Enigma-like family:
The Enigma LIM domain family is comprised of three
members: Enigma, ENH, and Cypher (mouse)/ZASP (human).
These subfamily members contain a single PDZ domain at
the N-terminus and three LIM domains at the C-terminus.
Enigma was initially characterized in humans and is
expressed in multiple tissues, such as skeletal muscle,
heart, bone and brain. The third LIM domain
specifically interacts with the insulin receptor and
the second LIM domain interacts with the receptor
tyrosine kinase Ret and the adaptor protein APS. Thus
Enigma is implicated in signal transduction processes,
such as mitogenic activity, insulin related actin
organization, and glucose metabolism. The second
member, ENH protein, was first identified in rat brain.
It has been shown that ENH interacts with protein
kinase D1 (PKD1) via its LIM domains and forms a
complex with PKD1 and the alpha1C subunit of cardiac
L-type voltage-gated calcium channel in rat neonatal
cardiomyocytes. The N-terminal PDZ domain interacts
with alpha-actinin at the Z-line. ZASP/Cypher is
required for maintenance of Z-line structure during
muscle contraction, but not required for Z-line
assembly. In heart, Cypher/ZASP plays a structural role
through its interaction with cytoskeletal Z-line
proteins. In addition, there is increasing evidence
that Cypher/ZASP also performs signaling functions.
Studies reveal that Cypher/ZASP interacts with and
directs PKC to the Z-line, where PKC phosphorylates
downstream signaling targets. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 52
Score = 42.5 bits (100), Expect = 1e-05
Identities = 19/54 (35%), Positives = 32/54 (59%), Gaps = 2/54 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+RC++ E ++++ + WH CFVCA C +P +F+ +G YCE D+
Sbjct: 1 CARCHKKILGE--VMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 42.5 bits (100), Expect = 1e-05
Identities = 20/52 (38%), Positives = 27/52 (51%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + I V+ AL + WHV FVCA C++P + + G YCE Y
Sbjct: 1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52
Score = 34.4 bits (79), Expect = 0.010
Identities = 20/66 (30%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C C++ I G++ AL + W HV FVCA C++P + + G
Sbjct: 1 CARCHKKILGEVMHALKQTW--------------HVSCFVCAACKQPIGNSLFHMEDGEP 46
Query: 440 YCETHY 445
YCE Y
Sbjct: 47 YCEKDY 52
Score = 30.1 bits (68), Expect = 0.28
Identities = 12/26 (46%), Positives = 16/26 (61%)
Query: 128 WHQQCFVCAQCFRPFPGGIFYEFEGE 153
WH CFVCA C +P +F+ +GE
Sbjct: 20 WHVSCFVCAACKQPIGNSLFHMEDGE 45
Score = 28.6 bits (64), Expect = 1.0
Identities = 12/41 (29%), Positives = 19/41 (46%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
++G V+ A+ WH CF C C + + + F G C
Sbjct: 8 ILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYC 48
>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 = 41.9 bits (98), Expect = 2e-05
Identities = 21/50 (42%), Positives = 27/50 (54%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCET 329
C C++PI R +TA+GK +H EHFVCA C K E+ YC
Sbjct: 1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHN 50
Score = 33.8 bits (77), Expect = 0.017
Identities = 16/44 (36%), Positives = 21/44 (47%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
+ GR I AM +HP+ F C C K+L F + CH C
Sbjct: 8 ITGRCITAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNC 51
Score = 27.6 bits (61), Expect = 2.9
Identities = 20/64 (31%), Positives = 24/64 (37%), Gaps = 14/64 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C C + I G TA+ GK +H EHFVCA C K E+
Sbjct: 1 CSGCQKPITGRCITAM--------------GKKFHPEHFVCAFCLKQLNKGTFKEQNDKP 46
Query: 440 YCET 443
YC
Sbjct: 47 YCHN 50
>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 = 41.3 bits (97), Expect = 4e-05
Identities = 18/52 (34%), Positives = 28/52 (53%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + I R + ALG+ +H E F C++C+K +E+KG +C Y
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKCY 52
Score = 32.5 bits (74), Expect = 0.044
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
GR + A+ ++HP+ F C C K L + GF +G C +C
Sbjct: 10 GRYLVALGRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFCPKC 51
Score = 31.7 bits (72), Expect = 0.072
Identities = 19/66 (28%), Positives = 29/66 (43%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C CN++I G A LG+ +H E F C++C+K +E+KG
Sbjct: 1 CAQCNKIIRGRYLVA--------------LGRSYHPEEFTCSQCKKVLDEGGFFEEKGSI 46
Query: 440 YCETHY 445
+C Y
Sbjct: 47 FCPKCY 52
Score = 28.2 bits (63), Expect = 1.4
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELN 246
C +C+ +I + L G YHP F C+ C L+
Sbjct: 1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLD 35
Score = 27.8 bits (62), Expect = 1.8
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 26 GELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
G +H + F C+QC + G F+E +G +C
Sbjct: 17 GRSYHPEEFTCSQCKKVLDEGGFFEEKGSIFC 48
>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 = 40.8 bits (96), Expect = 5e-05
Identities = 20/49 (40%), Positives = 26/49 (53%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCE 328
C C +PI R +TA+G+ +H EHFVCA C K E+ YC
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCH 49
Score = 33.1 bits (76), Expect = 0.027
Identities = 17/47 (36%), Positives = 24/47 (51%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
G+ + GR I AM +HP+ F C C K+L+ F + CH C
Sbjct: 5 GKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPC 51
Score = 31.9 bits (73), Expect = 0.073
Identities = 11/35 (31%), Positives = 16/35 (45%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELN 246
C C I + + G +HP HF C C +L+
Sbjct: 1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLS 35
Score = 26.5 bits (59), Expect = 5.1
Identities = 13/36 (36%), Positives = 18/36 (50%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCE 442
+ +G+ +H EHFVCA C K E+ YC
Sbjct: 14 TAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCH 49
Score = 26.1 bits (58), Expect = 9.2
Identities = 12/37 (32%), Positives = 19/37 (51%)
Query: 22 VNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
+ + G +H + FVCA C + G F E + + YC
Sbjct: 13 ITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCH 49
>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 = 40.7 bits (96), Expect = 6e-05
Identities = 17/48 (35%), Positives = 20/48 (41%), Gaps = 1/48 (2%)
Query: 280 CGACRRPIEE-RVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAY 326
C C+ I R ++ALG WH E F C C KP H Y
Sbjct: 1 CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
Score = 40.3 bits (95), Expect = 6e-05
Identities = 17/42 (40%), Positives = 22/42 (52%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
GR + A+ A WHP+CFRC C K +A+ F S C
Sbjct: 11 GRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSC 52
Score = 31.5 bits (72), Expect = 0.086
Identities = 12/49 (24%), Positives = 19/49 (38%), Gaps = 1/49 (2%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKY 56
C+ C + ++ G +WH +CF C C +P F Y
Sbjct: 1 CAGCKSEIGHGRFL-SALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
Score = 30.7 bits (70), Expect = 0.19
Identities = 13/34 (38%), Positives = 13/34 (38%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAY 440
S LG WH E F C C KP H Y
Sbjct: 15 SALGAVWHPECFRCHACRKPIAEHEFSVSGNDPY 48
Score = 29.1 bits (66), Expect = 0.72
Identities = 9/25 (36%), Positives = 11/25 (44%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYE 149
G WH +CF C C +P F
Sbjct: 18 GAVWHPECFRCHACRKPIAEHEFSV 42
>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 = 40.5 bits (94), Expect = 6e-05
Identities = 20/51 (39%), Positives = 28/51 (54%), Gaps = 1/51 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
CSRC + EKI+ + G+ WH+ CF CA+C + E EG YC+
Sbjct: 1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50
Score = 30.8 bits (69), Expect = 0.19
Identities = 13/34 (38%), Positives = 14/34 (41%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHECNA 200
WH CFRC C K L +G C C A
Sbjct: 21 WHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54
Score = 29.7 bits (66), Expect = 0.48
Identities = 17/43 (39%), Positives = 23/43 (53%), Gaps = 1/43 (2%)
Query: 289 ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
E+++ A GK WH F CA+C K EK+G YC+ Y
Sbjct: 12 EKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
Score = 28.9 bits (64), Expect = 0.88
Identities = 15/36 (41%), Positives = 18/36 (50%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
GK WH F CA+C K EK+G YC+ Y
Sbjct: 18 GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53
Score = 27.4 bits (60), Expect = 3.0
Identities = 12/29 (41%), Positives = 15/29 (51%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEGE 153
G WH+ CF CA+C + E EGE
Sbjct: 18 GKPWHKNCFRCAKCGKSLESTTLTEKEGE 46
>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 = 41.0 bits (96), Expect = 7e-05
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 2/57 (3%)
Query: 276 GIPICGACRRPI-EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
+P+C +C + I + + + AL WH + F C C L H +YEK G +C+ Y
Sbjct: 18 VLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGAS-LSHWYYEKDGRLFCKKDY 73
Score = 31.8 bits (72), Expect = 0.15
Identities = 11/26 (42%), Positives = 18/26 (69%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELA 182
G+ ++A+N++WH CFRC C L+
Sbjct: 32 GQYLQALNSDWHADCFRCCECGASLS 57
Score = 31.4 bits (71), Expect = 0.19
Identities = 14/37 (37%), Positives = 18/37 (48%), Gaps = 1/37 (2%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
L WH + F C C L H +YEK G +C+ Y
Sbjct: 38 LNSDWHADCFRCCECGAS-LSHWYYEKDGRLFCKKDY 73
Score = 27.9 bits (62), Expect = 3.6
Identities = 15/54 (27%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+ C + + + N + WH CF C +C +YE +GR +C+ D+
Sbjct: 22 CASCGQSIYDGQYLQALNSD-WHADCFRCCECGASLSHW-YYEKDGRLFCKKDY 73
>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 = 39.6 bits (92), Expect = 1e-04
Identities = 19/52 (36%), Positives = 26/52 (50%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C++ I ++ AL WHV F CA C+ P Y ++G YCE Y
Sbjct: 1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 38.8 bits (90), Expect = 2e-04
Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 2/54 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C++C + E I+++ WH CF CA C P FY EG YCE D+
Sbjct: 1 CAKCKKKITGE--IMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 32.3 bits (73), Expect = 0.046
Identities = 14/33 (42%), Positives = 17/33 (51%)
Query: 413 WHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
WHV F CA C+ P Y ++G YCE Y
Sbjct: 20 WHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52
Score = 30.0 bits (67), Expect = 0.33
Identities = 11/43 (25%), Positives = 19/43 (44%)
Query: 153 EFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
+ + G ++ A+ WH CF C C + + F +G C
Sbjct: 6 KKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYC 48
Score = 28.8 bits (64), Expect = 0.85
Identities = 12/26 (46%), Positives = 12/26 (46%)
Query: 128 WHQQCFVCAQCFRPFPGGIFYEFEGE 153
WH CF CA C P FY EG
Sbjct: 20 WHVHCFTCAACKTPIRNRAFYMEEGA 45
>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 = 39.7 bits (93), Expect = 1e-04
Identities = 18/54 (33%), Positives = 26/54 (48%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C +C E E + +++H CF C QC G FY +G+ YCE D+
Sbjct: 1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54
Score = 27.8 bits (62), Expect = 2.2
Identities = 12/36 (33%), Positives = 15/36 (41%)
Query: 162 AMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
AM+ +H CF C C L F G+ C E
Sbjct: 17 AMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEE 52
>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM
domains protein (FHL). The fourth LIM domain of Four
and a half LIM domains protein (FHL): LIM-only protein
family consists of five members, designated FHL1, FHL2,
FHL3, FHL5 and LIMPETin. The first four members are
composed of four complete LIM domains arranged in tandem
and an N-terminal single zinc finger domain with a
consensus sequence equivalent to the C-terminal half of
a LIM domain. LIMPETin is an exception, containing six
LIM domains. FHL1, 2 and 3 are predominantly expressed
in muscle tissues, and FHL5 is highly expressed in male
germ cells. FHL proteins exert their roles as
transcription co-activators or co-repressors through a
wide array of interaction partners. For example, FHL1
binds to Myosin-binding protein C, regulating myosin
filament formation and sarcomere assembly. FHL2 has
shown to interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. FHL3 interacts with many
transcription factors, such as CREB, BKLF/KLF3, CtBP2,
MyoD, and MZF_1. FHL5 is a tissue-specific coactivator
of CREB/CREM family transcription factors. LIM domains
are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 56
Score = 39.2 bits (92), Expect = 2e-04
Identities = 22/68 (32%), Positives = 25/68 (36%), Gaps = 15/68 (22%)
Query: 135 CAQCFRP---FPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQG 191
CA C +P G F FE WH CF C CS L GF+ +
Sbjct: 1 CAACTKPITGLGGAKFISFE------------ERQWHSDCFNCGKCSVSLVGQGFLTQRD 48
Query: 192 RALCHECN 199
LC EC
Sbjct: 49 EILCPECG 56
>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 = 39.2 bits (91), Expect = 2e-04
Identities = 21/52 (40%), Positives = 25/52 (48%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + I + ALGK WH E F CA C+ E+KG YCE Y
Sbjct: 1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEICY 52
Score = 37.3 bits (86), Expect = 0.001
Identities = 15/42 (35%), Positives = 23/42 (54%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
G + A+ +WHP+ F C HC +A +GF+ +G C C
Sbjct: 10 GPFLVALGKSWHPEEFNCAHCKSSMAYIGFVEEKGALYCEIC 51
Score = 36.1 bits (83), Expect = 0.002
Identities = 25/66 (37%), Positives = 27/66 (40%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C CNQVI G A LGK WH E F CA C+ E+KG
Sbjct: 1 CATCNQVIRGPFLVA--------------LGKSWHPEEFNCAHCKSSMAYIGFVEEKGAL 46
Query: 440 YCETHY 445
YCE Y
Sbjct: 47 YCEICY 52
>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 = 39.3 bits (92), Expect = 2e-04
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 2/49 (4%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKY 56
C C + E E +V++ G+ +H +CFVC+ C +PFP G F G++
Sbjct: 4 CDSCQDFVEGE--VVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKEC 50
Score = 38.5 bits (90), Expect = 3e-04
Identities = 16/34 (47%), Positives = 24/34 (70%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPF 313
C +C+ +E VV+ALGK +H + FVC+ C +PF
Sbjct: 4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQPF 37
Score = 34.2 bits (79), Expect = 0.011
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSK 179
+FV G V+ A+ +HPKCF C C +
Sbjct: 8 QDFVEGEVVSALGKTYHPKCFVCSVCRQ 35
Score = 31.2 bits (71), Expect = 0.12
Identities = 11/21 (52%), Positives = 15/21 (71%)
Query: 125 GGAWHQQCFVCAQCFRPFPGG 145
G +H +CFVC+ C +PFP G
Sbjct: 20 GKTYHPKCFVCSVCRQPFPPG 40
Score = 30.8 bits (70), Expect = 0.20
Identities = 15/51 (29%), Positives = 23/51 (45%), Gaps = 14/51 (27%)
Query: 377 GNLCFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPF 427
G C C + G++ +AL GK +H + FVC+ C +PF
Sbjct: 1 GTKCDSCQDFVEGEVVSAL--------------GKTYHPKCFVCSVCRQPF 37
Score = 26.2 bits (58), Expect = 8.1
Identities = 9/31 (29%), Positives = 15/31 (48%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCG 242
C C ++ + + G+ YHP F C+ C
Sbjct: 4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCR 34
>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 = 39.1 bits (91), Expect = 2e-04
Identities = 20/53 (37%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 330
C +C PIE +R V AL ++H + F C RC G Y K G +C+ H
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLH 53
Score = 31.0 bits (70), Expect = 0.14
Identities = 16/51 (31%), Positives = 23/51 (45%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C C E ++ V + +H QCF C +C G FY GR +C+
Sbjct: 1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51
Score = 30.6 bits (69), Expect = 0.19
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
R ++A+N N+H +CF C C+ L F GR C
Sbjct: 13 RWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFC 50
Score = 27.9 bits (62), Expect = 1.9
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 444
L ++H + F C RC G Y K G +C+ H
Sbjct: 18 LNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCKLH 53
>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 = 39.0 bits (91), Expect = 2e-04
Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 280 CGACRRPI-EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C CR I + + V AL + WH + F C+ C L + ++EK G YC Y
Sbjct: 1 CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDS-LSNWYFEKDGKLYCRKDY 52
Score = 33.6 bits (77), Expect = 0.017
Identities = 13/43 (30%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 403 HFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
L + WH + F C+ C L + ++EK G YC Y
Sbjct: 11 SQYVQALNQDWHCDCFRCSVCSDS-LSNWYFEKDGKLYCRKDY 52
Score = 29.4 bits (66), Expect = 0.58
Identities = 11/25 (44%), Positives = 16/25 (64%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKEL 181
+ ++A+N +WH CFRC CS L
Sbjct: 11 SQYVQALNQDWHCDCFRCSVCSDSL 35
Score = 27.8 bits (62), Expect = 2.1
Identities = 14/54 (25%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+ C + V + + WH CF C+ C ++E +G+ YC D+
Sbjct: 1 CAGCRGKILDSQ-YVQALNQDWHCDCFRCSVCSDSLSNW-YFEKDGKLYCRKDY 52
>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain
only protein 4). The second LIM domain of LMO4 (LIM
domain only protein 4): LMO4 is a nuclear protein that
plays important roles in transcriptional regulation and
development. LMO4 is involved in various functions in
tumorigenesis and cellular differentiation. LMO4
proteins regulate gene expression by interacting with a
wide variety of transcription factors and cofactors to
form large transcription complexes. It can interact
with Smad proteins, and associate with the promoter of
the PAI-1 (plasminogen activator inhibitor-1) gene in a
TGFbeta (transforming growth factor beta)-dependent
manner. LMO4 can also form a complex with transcription
regulator CREB (cAMP response element-binding protein)
and interact with CLIM1 and CLIM2. In breast tissue,
LMO4 interacts with multiple proteins, including the
cofactor CtIP [CtBP (C-terminal binding
protein)-interacting protein], the breast and ovarian
tumor suppressor BRCA1 (breast-cancer susceptibility
gene 1) and the LIM-domain-binding protein LDB1.
Functionally, LMO4 is shown to repress BRCA1-mediated
transcription activation, thus invoking a potential
role for LMO4 as a negative regulator of BRCA1 in
sporadic breast cancer. LMO4 also forms complex to
both ERa (oestrogen receptor alpha), MTA1 (metastasis
tumor antigen 1), and HDACs (histone deacetylases),
implying that LMO4 is also a component of the MTA1
corepressor complex. Over-expressed LMO4 represses ERa
transactivation functions in an HDAC-dependent manner,
and contributes to the process of breast cancer
progression by allowing the development of Era-negative
phenotypes. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 55
Score = 38.2 bits (89), Expect = 5e-04
Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCF-RPFPGGIFYEFEGRKYCEHDF 61
CS C + E ++ + G ++H +CF C+ C + PG F+ G +CEHD
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHDR 55
Score = 29.4 bits (66), Expect = 0.58
Identities = 17/53 (32%), Positives = 26/53 (49%), Gaps = 3/53 (5%)
Query: 280 CGACRR--PIEERVVTALGKHWHVEHFVCARCEKPFL-GHRHYEKKGLAYCET 329
C AC + P E V+ A G +H++ F C+ C + G R + G +CE
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEH 53
Score = 25.9 bits (57), Expect = 9.5
Identities = 13/36 (36%), Positives = 16/36 (44%), Gaps = 2/36 (5%)
Query: 212 CHKCHGLIDDKPLKFR--GEVYHPYHFNCTSCGTEL 245
C C I L R G VYH F C++C +L
Sbjct: 1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQL 36
>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 = 38.2 bits (89), Expect = 5e-04
Identities = 20/51 (39%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 278 PICGACRRPI-EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
P C AC I + A G+HWH++HF C CE G R+ ++G YC
Sbjct: 1 PRCSACDEIIFADECTEAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
Score = 35.1 bits (81), Expect = 0.006
Identities = 14/32 (43%), Positives = 20/32 (62%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
G+HWH++HF C CE G R+ ++G YC
Sbjct: 20 GRHWHMKHFCCFECECQLGGQRYIMREGRPYC 51
Score = 27.0 bits (60), Expect = 4.0
Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
CS C+E +E + G WH + F C +C G + EGR YC H F
Sbjct: 3 CSACDEIIFADECT-EAEGRHWHMKHFCCFECECQLGGQRYIMREGRPYCCHCF 55
>gnl|CDD|188816 cd09432, LIM6_LIMPETin, The sixth LIM domain of protein LIMPETin.
The sixth LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 56
Score = 37.8 bits (88), Expect = 6e-04
Identities = 23/67 (34%), Positives = 26/67 (38%), Gaps = 15/67 (22%)
Query: 135 CAQCFRPFPG---GIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQG 191
CA C +P G F FE +WH CF C C L GFI G
Sbjct: 1 CAACGKPITGIGGTKFISFEDR------------HWHNDCFNCAGCRTSLVGKGFITDGG 48
Query: 192 RALCHEC 198
R LC +C
Sbjct: 49 RILCPDC 55
Score = 29.8 bits (67), Expect = 0.41
Identities = 13/40 (32%), Positives = 20/40 (50%), Gaps = 4/40 (10%)
Query: 280 CGACRRPIE----ERVVTALGKHWHVEHFVCARCEKPFLG 315
C AC +PI + ++ +HWH + F CA C +G
Sbjct: 1 CAACGKPITGIGGTKFISFEDRHWHNDCFNCAGCRTSLVG 40
Score = 27.8 bits (62), Expect = 2.0
Identities = 13/38 (34%), Positives = 15/38 (39%)
Query: 20 KIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
K ++ WH CF CA C G F GR C
Sbjct: 15 KFISFEDRHWHNDCFNCAGCRTSLVGKGFITDGGRILC 52
Score = 25.9 bits (57), Expect = 9.5
Identities = 7/11 (63%), Positives = 7/11 (63%)
Query: 128 WHQQCFVCAQC 138
WH CF CA C
Sbjct: 24 WHNDCFNCAGC 34
>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 = 37.7 bits (87), Expect = 8e-04
Identities = 20/57 (35%), Positives = 27/57 (47%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLFG 336
C C++PI VT + WH E FVC C+K G R + AYC + L+
Sbjct: 1 CVQCKKPITTGGVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
Score = 30.0 bits (67), Expect = 0.34
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 413 WHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLFG 450
WH E FVC C+K G R + AYC + L+
Sbjct: 20 WHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
Score = 30.0 bits (67), Expect = 0.47
Identities = 14/38 (36%), Positives = 20/38 (52%)
Query: 29 WHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFHVLFA 66
WH++CFVC C + G F + YC + F L+A
Sbjct: 20 WHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCNLYA 57
>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 = 37.2 bits (87), Expect = 0.001
Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 278 PICGACRRPI-EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
P C AC I A GK+WH++HF C +C++P G R+ ++G YC Y
Sbjct: 1 PRCAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
Score = 33.3 bits (77), Expect = 0.026
Identities = 15/39 (38%), Positives = 24/39 (61%)
Query: 408 TLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 446
GK+WH++HF C +C++P G R+ ++G YC Y
Sbjct: 18 AEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCYE 56
Score = 31.0 bits (71), Expect = 0.15
Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 5/49 (10%)
Query: 150 FEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
F GE+ +A NWH K F C C + L ++ +G+ C +C
Sbjct: 11 FSGEYT-----QAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDC 54
>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 = 37.0 bits (86), Expect = 0.001
Identities = 17/52 (32%), Positives = 22/52 (42%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEH 59
C RC E E + +++H CF C C G FY E + YCE
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEP 52
Score = 29.3 bits (66), Expect = 0.59
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 2/54 (3%)
Query: 280 CGACRRPI--EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
CG C + E TA+ + +HV+ F C C G Y + AYCE Y
Sbjct: 1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 27.8 bits (62), Expect = 2.1
Identities = 13/40 (32%), Positives = 19/40 (47%)
Query: 406 CSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
C+ + + +HV+ F C C G Y + AYCE Y
Sbjct: 15 CTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54
Score = 27.8 bits (62), Expect = 2.6
Identities = 12/37 (32%), Positives = 18/37 (48%)
Query: 162 AMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
AM+ +H CF C C+ +L F + +A C C
Sbjct: 17 AMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPC 53
>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 = 37.0 bits (86), Expect = 0.001
Identities = 22/53 (41%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 330
C C PIE +R + ALG WH FVCA C G Y KK C+ H
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNH 53
Score = 34.7 bits (80), Expect = 0.007
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C+ E ++ + + G WH CFVCA C G FY + + C
Sbjct: 1 CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 31.3 bits (71), Expect = 0.11
Identities = 12/38 (31%), Positives = 17/38 (44%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
R ++A+ WH CF C C L F + + LC
Sbjct: 13 RFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50
Score = 28.9 bits (65), Expect = 0.89
Identities = 15/36 (41%), Positives = 16/36 (44%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 444
LG WH FVCA C G Y KK C+ H
Sbjct: 18 LGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNH 53
Score = 27.0 bits (60), Expect = 4.0
Identities = 12/24 (50%), Positives = 12/24 (50%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFY 148
G WH CFVCA C G FY
Sbjct: 19 GHTWHDTCFVCAVCHVNLEGQTFY 42
>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 = 36.9 bits (86), Expect = 0.001
Identities = 20/53 (37%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIEE-RVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + I+ + + AL K WHV F C C K G + K G YCE Y
Sbjct: 1 CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52
Score = 30.4 bits (69), Expect = 0.23
Identities = 10/26 (38%), Positives = 16/26 (61%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELA 182
G+ + A++ WH CF+C+ C K L
Sbjct: 11 GQALLALDKQWHVWCFKCKECGKVLT 36
Score = 28.4 bits (64), Expect = 1.2
Identities = 16/37 (43%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
L K WHV F C C K G + K G YCE Y
Sbjct: 17 LDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 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 = 36.7 bits (85), Expect = 0.001
Identities = 21/65 (32%), Positives = 28/65 (43%), Gaps = 9/65 (13%)
Query: 135 CAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRAL 194
CA C +P G F G+ + + WH CF+C CS L GF + L
Sbjct: 1 CAACNKPITG---------FGGGKYVSFEDRQWHQPCFKCSRCSVSLVGAGFFPDGDQIL 51
Query: 195 CHECN 199
C +CN
Sbjct: 52 CRDCN 56
Score = 26.3 bits (58), Expect = 7.7
Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 4/40 (10%)
Query: 280 CGACRRPI----EERVVTALGKHWHVEHFVCARCEKPFLG 315
C AC +PI + V+ + WH F C+RC +G
Sbjct: 1 CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSLVG 40
>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 = 36.8 bits (85), Expect = 0.001
Identities = 17/51 (33%), Positives = 27/51 (52%), Gaps = 1/51 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C RC + EKI+ + G+ WH+ CF CA+C + + +G YC+
Sbjct: 1 CPRCGKSVYAAEKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50
Score = 29.5 bits (66), Expect = 0.53
Identities = 15/43 (34%), Positives = 17/43 (39%), Gaps = 1/43 (2%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHECNA 200
++I A WH CFRC C K L G C C A
Sbjct: 13 KIIGAGKP-WHKNCFRCAKCGKSLESTTLADKDGEIYCKGCYA 54
Score = 27.2 bits (60), Expect = 3.2
Identities = 16/43 (37%), Positives = 22/43 (51%), Gaps = 1/43 (2%)
Query: 289 ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
E+++ A GK WH F CA+C K +K G YC+ Y
Sbjct: 12 EKIIGA-GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 26.4 bits (58), Expect = 6.7
Identities = 14/36 (38%), Positives = 17/36 (47%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
GK WH F CA+C K +K G YC+ Y
Sbjct: 18 GKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCY 53
Score = 26.0 bits (57), Expect = 8.9
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEGE 153
G WH+ CF CA+C + + +GE
Sbjct: 18 GKPWHKNCFRCAKCGKSLESTTLADKDGE 46
>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 = 36.5 bits (84), Expect = 0.002
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 157 GRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
G + A+ +WHP+ F C +C LAD+ F+ Q C C
Sbjct: 10 GPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENC 51
Score = 34.6 bits (79), Expect = 0.007
Identities = 18/52 (34%), Positives = 22/52 (42%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
CG C I + ALG+ WH E F C C E++ YCE Y
Sbjct: 1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52
Score = 29.2 bits (65), Expect = 0.58
Identities = 19/66 (28%), Positives = 23/66 (34%), Gaps = 14/66 (21%)
Query: 380 CFVCNQVIGGDLFTALNKAWCVHHFACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLA 439
C CN +I G AL G+ WH E F C C E++
Sbjct: 1 CGHCNNIIRGPFLVAL--------------GRSWHPEEFTCHYCHTSLADVSFVEEQNNV 46
Query: 440 YCETHY 445
YCE Y
Sbjct: 47 YCENCY 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 = 36.2 bits (83), Expect = 0.002
Identities = 20/55 (36%), Positives = 26/55 (47%), Gaps = 2/55 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
C C P+E ++ + ALG WH F+CA C G Y KK C+ H H
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55
Score = 35.8 bits (82), Expect = 0.003
Identities = 17/55 (30%), Positives = 25/55 (45%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
C C+ E +K + + G WH CF+CA C G FY + + C+ H
Sbjct: 1 CHGCDFPVEAGDKFIEALGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55
Score = 29.2 bits (65), Expect = 0.72
Identities = 15/38 (39%), Positives = 17/38 (44%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 446
LG WH F+CA C G Y KK C+ H H
Sbjct: 18 LGHTWHDTCFICAVCHVNLEGQPFYSKKDKPLCKKHAH 55
Score = 26.2 bits (57), Expect = 9.2
Identities = 11/24 (45%), Positives = 12/24 (50%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFY 148
G WH CF+CA C G FY
Sbjct: 19 GHTWHDTCFICAVCHVNLEGQPFY 42
>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 = 35.7 bits (82), Expect = 0.003
Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 2/55 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 332
C C PIE +R + ALG WH FVC+ C + G + KK C+ H H
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55
Score = 31.9 bits (72), Expect = 0.079
Identities = 15/55 (27%), Positives = 24/55 (43%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFH 62
C C E ++ + + G WH CFVC+ C G F+ + + C+ H
Sbjct: 1 CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55
Score = 28.0 bits (62), Expect = 1.8
Identities = 14/38 (36%), Positives = 18/38 (47%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYH 446
LG WH FVC+ C + G + KK C+ H H
Sbjct: 18 LGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKHAH 55
Score = 27.2 bits (60), Expect = 3.7
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
R ++A+ WH CF C C + L F + + LC
Sbjct: 13 RFLEALGHTWHDTCFVCSVCCESLEGQTFFSKKDKPLC 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 = 35.4 bits (82), Expect = 0.003
Identities = 19/51 (37%), Positives = 23/51 (45%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 330
C C I VV A K+ H E FVCA C ++ + YCETH
Sbjct: 1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCETH 51
Score = 27.0 bits (60), Expect = 4.5
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 444
K+ H E FVCA C ++ + YCETH
Sbjct: 17 DKNRHPECFVCADCGLNLKNKGYFFIEDELYCETH 51
Score = 26.2 bits (58), Expect = 8.4
Identities = 14/35 (40%), Positives = 21/35 (60%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGF 186
G ++G V+KA + N HP+CF C C L + G+
Sbjct: 5 GNGIVGVVVKARDKNRHPECFVCADCGLNLKNKGY 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 = 35.4 bits (82), Expect = 0.004
Identities = 12/39 (30%), Positives = 19/39 (48%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
++ +WH C RCE C K L +G+ C++C
Sbjct: 14 KTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKC 52
Score = 34.6 bits (80), Expect = 0.007
Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 1/52 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEH 59
C +C + EK S G WH+ C C +C + G E EG+ YC
Sbjct: 1 CPKCGKPVYFAEKKT-SLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51
Score = 33.9 bits (78), Expect = 0.014
Identities = 17/53 (32%), Positives = 25/53 (47%), Gaps = 1/53 (1%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C +P+ T+LG+ WH C +C+K +H E +G YC Y
Sbjct: 1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
Score = 30.4 bits (69), Expect = 0.26
Identities = 13/37 (35%), Positives = 18/37 (48%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
LG+ WH C +C+K +H E +G YC Y
Sbjct: 17 LGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53
>gnl|CDD|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM
domains protein 3 (FHL3). The second LIM domain of
Four and a half LIM domains protein 3 (FHL3): FHL3 is
highly expressed in the skeleton and cardiac muscles
and possesses the transactivation and repression
activities. FHL3 interacts with many transcription
factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and
MZF_1. Moreover, FHL3 interacts with alpha- and
beta-subunits of the muscle alpha7beta1 integrin
receptor. FHL3 was also proved to possess the
auto-activation ability and was confirmed that the
second zinc finger motif in fourth LIM domain was
responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 35.2 bits (81), Expect = 0.006
Identities = 14/50 (28%), Positives = 22/50 (44%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C + P + + G+ WH+ CF+C C +P F + YC
Sbjct: 4 CVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53
Score = 26.7 bits (59), Expect = 6.2
Identities = 9/25 (36%), Positives = 13/25 (52%)
Query: 117 GEDRQTLTGGAWHQQCFVCAQCFRP 141
G + G WH+ CF+C C +P
Sbjct: 14 GSRKLEYEGQTWHEHCFICHGCEQP 38
>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4
family. The second LIM domain of Lhx3-Lhx4 family:
Lhx3 and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
The LHX3 and LHX4 LIM-homeodomain transcription factors
play essential roles in pituitary gland and nervous
system development. Although LHX3 and LHX4 share marked
sequence homology, the genes have different expression
patterns. They play overlapping, but distinct functions
during the establishment of the specialized cells of
the mammalian pituitary gland and the nervous system.
Lhx3 proteins have been demonstrated the ability to
directly bind to the promoters/enhancers of several
pituitary hormone gene promoters to cause increased
transcription.Lhx3a and Lhx3b, whose mRNAs have
distinct temporal expression profiles during
development, are two isoforms of Lhx3. LHX4 plays
essential roles in pituitary gland and nervous system
development. In mice, the lhx4 gene is expressed in the
developing hindbrain, cerebral cortex, pituitary gland,
and spinal cord. LHX4 shows significant sequence
similarity to LHX3, particularly to isoforms Lhx3a. In
gene regulation experiments, the LHX4 protein exhibits
regulation roles towards pituitary genes, acting on
their promoters/enhancers. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 56
Score = 35.0 bits (81), Expect = 0.006
Identities = 17/56 (30%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPF-PGGIFYEFEGRKY-CEHDF 61
C+ C+EG P + + + ++H +CF C C R G FY E + C+ D+
Sbjct: 1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56
>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 = 35.3 bits (82), Expect = 0.006
Identities = 13/29 (44%), Positives = 17/29 (58%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALC 195
WHP CF CE C++ L DL + G+ C
Sbjct: 26 WHPGCFVCETCNELLVDLIYFYHDGKIYC 54
Score = 29.9 bits (68), Expect = 0.36
Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 4/58 (6%)
Query: 8 CSRCNEGFEPEEKIVN----SNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C +C E P E V WH CFVC C I++ +G+ YC +
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
Score = 27.6 bits (62), Expect = 3.2
Identities = 18/58 (31%), Positives = 23/58 (39%), Gaps = 6/58 (10%)
Query: 280 CGACRRPIE--ERVVTAL----GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C+ PI E V A WH FVC C + + ++ G YC HY
Sbjct: 1 CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58
>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 = 34.9 bits (80), Expect = 0.008
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRH-YEKKGLAYCETHYHQLF 335
C C + I +R++ A GK +H + F C C+ P G ++ +C YH+ +
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRY 57
Score = 32.2 bits (73), Expect = 0.074
Identities = 17/61 (27%), Positives = 33/61 (54%), Gaps = 3/61 (4%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRK-YCEHDFHVLFA 66
C+ C++ ++++ + G+ +H QCF C C P G F + + +C +D+H +A
Sbjct: 1 CAVCDQKIT--DRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYA 58
Query: 67 P 67
P
Sbjct: 59 P 59
Score = 29.1 bits (65), Expect = 0.82
Identities = 14/34 (41%), Positives = 16/34 (47%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTEL 245
C C I D+ LK G+ YHP F C C L
Sbjct: 1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPL 34
Score = 28.4 bits (63), Expect = 1.8
Identities = 13/41 (31%), Positives = 20/41 (48%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGR 192
+ + R++KA ++HP+CF C C L FI Q
Sbjct: 5 DQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQAN 45
Score = 28.0 bits (62), Expect = 2.5
Identities = 11/24 (45%), Positives = 13/24 (54%)
Query: 124 TGGAWHQQCFVCAQCFRPFPGGIF 147
TG ++H QCF C C P G F
Sbjct: 16 TGKSYHPQCFTCVVCKCPLEGESF 39
>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 = 34.7 bits (80), Expect = 0.008
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWH--QQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C E P+ + V NG+ WH ++CF C+ C + G F G+ +C
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
Score = 29.3 bits (66), Expect = 0.78
Identities = 19/52 (36%), Positives = 25/52 (48%), Gaps = 4/52 (7%)
Query: 280 CGACRRPI--EERVVTALGKHWHVEH--FVCARCEKPFLGHRHYEKKGLAYC 327
C AC PI + + V G+HWH F C+ C+K LG K G +C
Sbjct: 1 CDACGEPIGPDVQRVAHNGQHWHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
Score = 26.6 bits (59), Expect = 7.3
Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 2/31 (6%)
Query: 167 WH--PKCFRCEHCSKELADLGFIRSQGRALC 195
WH +CF C +C K L F+ G+ C
Sbjct: 22 WHATEECFCCSNCKKSLLGQPFLPKNGQIFC 52
>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 = 34.6 bits (80), Expect = 0.009
Identities = 14/33 (42%), Positives = 19/33 (57%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKP 312
C C +PI + V ALG +H++ F C C KP
Sbjct: 1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGKP 33
Score = 30.0 bits (68), Expect = 0.41
Identities = 10/31 (32%), Positives = 18/31 (58%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELA 182
G+ + G+ ++A+ +H CF C C K +A
Sbjct: 5 GKPITGQFVRALGDVYHLDCFTCHDCGKPVA 35
Score = 28.0 bits (63), Expect = 2.1
Identities = 10/35 (28%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRP 42
C++C + + V + G+++H CF C C +P
Sbjct: 1 CAKCGKPITGQ--FVRALGDVYHLDCFTCHDCGKP 33
Score = 26.9 bits (60), Expect = 5.4
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 125 GGAWHQQCFVCAQCFRP 141
G +H CF C C +P
Sbjct: 17 GDVYHLDCFTCHDCGKP 33
>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 = 34.2 bits (79), Expect = 0.010
Identities = 10/30 (33%), Positives = 20/30 (66%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKEL 181
G ++ +++A+ ++HP CFRC C++ L
Sbjct: 5 GHLIMEMILQALGKSYHPGCFRCCVCNECL 34
Score = 26.9 bits (60), Expect = 4.6
Identities = 12/32 (37%), Positives = 16/32 (50%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEK 311
C C I E ++ ALGK +H F C C +
Sbjct: 1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNE 32
Score = 26.5 bits (59), Expect = 6.6
Identities = 13/35 (37%), Positives = 17/35 (48%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELN 246
C C LI + L+ G+ YHP F C C L+
Sbjct: 1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLD 35
>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 = 34.4 bits (79), Expect = 0.011
Identities = 18/48 (37%), Positives = 22/48 (45%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C +PI VT + WH E FVC+ C K G R + YC
Sbjct: 1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
Score = 31.7 bits (72), Expect = 0.086
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
WH +CF C CSK+LA F + + C +C
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQYYCVDC 51
Score = 30.6 bits (69), Expect = 0.20
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 29 WHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
WH +CFVC+ C + G F E + YC
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
Score = 27.5 bits (61), Expect = 2.7
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 128 WHQQCFVCAQCFRPFPGGIFYEFEGEF 154
WH +CFVC+ C + G F E ++
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQY 46
Score = 26.7 bits (59), Expect = 5.8
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 413 WHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
WH E FVC+ C K G R + YC
Sbjct: 20 WHSECFVCSSCSKKLAGQRFTAVEDQYYC 48
>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 = 34.1 bits (78), Expect = 0.012
Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 2/52 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWH--QQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C+ +PE + V+ N WH +CF+C+ C + G F EG +C
Sbjct: 1 CQGCHNAIDPEVQRVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFC 52
Score = 30.6 bits (69), Expect = 0.26
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 4/54 (7%)
Query: 280 CGACRRPI--EERVVTALGKHWHVEH--FVCARCEKPFLGHRHYEKKGLAYCET 329
C C I E + V+ HWH E F+C+ C K +G + +G+ +C
Sbjct: 1 CQGCHNAIDPEVQRVSYNNFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFCSV 54
Score = 27.2 bits (60), Expect = 4.3
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 2/34 (5%)
Query: 164 NANWH--PKCFRCEHCSKELADLGFIRSQGRALC 195
N +WH P+CF C CSK L F+ +G C
Sbjct: 19 NFHWHAEPECFLCSCCSKCLIGQKFMPVEGMVFC 52
>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 = 34.4 bits (79), Expect = 0.012
Identities = 20/61 (32%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIF-YEFEGRKYCEHDFHVLFA 66
CS C++ ++I+ + G+ +H QCF C C + G F + + +C DFH FA
Sbjct: 1 CSVCSKPIL--DRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFA 58
Query: 67 P 67
P
Sbjct: 59 P 59
Score = 31.7 bits (72), Expect = 0.090
Identities = 14/36 (38%), Positives = 20/36 (55%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLG 315
C C +PI +R++ A GK +H + F C C K G
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDG 36
Score = 31.0 bits (70), Expect = 0.20
Identities = 19/67 (28%), Positives = 29/67 (43%), Gaps = 8/67 (11%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTANDMNELYCLRC 271
C C I D+ L+ G+ YHP F C CG L+ +T + N+++C+
Sbjct: 1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIP--------FTVDATNQIHCIED 52
Query: 272 HDKMGIP 278
K P
Sbjct: 53 FHKKFAP 59
Score = 28.3 bits (63), Expect = 1.8
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 155 VIGRVIKAMNANWHPKCFRCEHCSKELADLGF 186
++ R+++A +HP+CF C C K L + F
Sbjct: 8 ILDRILRATGKPYHPQCFTCVVCGKSLDGIPF 39
>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 = 33.9 bits (78), Expect = 0.016
Identities = 12/33 (36%), Positives = 17/33 (51%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKP 312
C C+ I E ++ ALGK +H F C C +
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRR 33
Score = 31.6 bits (72), Expect = 0.089
Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 1/45 (2%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGF-IRSQGRALC 195
+ +I+A+ +HP CF C C + + D F + Q C
Sbjct: 5 QGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYC 49
Score = 31.6 bits (72), Expect = 0.10
Identities = 18/58 (31%), Positives = 31/58 (53%), Gaps = 8/58 (13%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELNSDAREVKSRPGYTANDMNELYCL 269
C KC G+I + ++ G+ YHP F C +CG + ++ + ++ NE+YCL
Sbjct: 1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDES--------FAVDEQNEVYCL 50
Score = 27.0 bits (60), Expect = 4.1
Identities = 16/55 (29%), Positives = 23/55 (41%), Gaps = 3/55 (5%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFE-GRKYCEHDF 61
C++C E I+ + G+ +H CF C C R F E YC D+
Sbjct: 1 CAKCQGVIT--EHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53
>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich
Protein 3 (CRP3/MLP). The second LIM domain of
Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich
proteins (CRPs) are characterized by the presence of
two LIM domains linked to short glycine-rich repeats
(GRRs). The CRP family members include CRP1, CRP2,
CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved
nuclear targeting signal (K/R-K/R-Y-G-P-K), which
supports the fact that these proteins function not only
in the cytoplasm but also in the nucleus. CRPs control
regulatory pathways during cellular differentiation,
and involve in complex transcription circuits, and the
organization as well as the arrangement of the
myofibrillar/cytoskeletal network.CRP3 also called
Muscle LIM Protein (MLP), which is a striated
muscle-specific factor that enhances myogenic
differentiation. The second LIM domain of CRP3/MLP
interacts with cytoskeletal protein beta-spectrin.
CRP3/MLP also interacts with the basic helix-loop-helix
myogenic transcription factors MyoD, myogenin, and MRF4
thereby increasing their affinity for specific DNA
regulatory elements. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 54
Score = 33.8 bits (77), Expect = 0.017
Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C RC + EK++ G+ WH+ CF CA C + + +G YC+
Sbjct: 1 CPRCGKSVYAAEKVMGG-GKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50
Score = 29.2 bits (65), Expect = 0.74
Identities = 13/34 (38%), Positives = 13/34 (38%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHECNA 200
WH CFRC C K L G C C A
Sbjct: 21 WHKTCFRCAICGKSLESTTVTDKDGELYCKVCYA 54
Score = 26.1 bits (57), Expect = 9.4
Identities = 18/54 (33%), Positives = 24/54 (44%), Gaps = 3/54 (5%)
Query: 280 CGACRRPI--EERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + + E+V+ GK WH F CA C K +K G YC+ Y
Sbjct: 1 CPRCGKSVYAAEKVMGG-GKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53
>gnl|CDD|188808 cd09424, LIM2_FHL1, The second LIM domain of Four and a half LIM
domains protein 1 (FHL1). The second LIM domain of
Four and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth,
differentiation, and sarcomere assembly by acting as a
modulator of transcription factors. Defects in FHL1
gene are responsible for a number of Muscular
dystrophy-like muscle disorders. It has been detected
that FHL1 binds to Myosin-binding protein C, regulating
myosin filament formation and sarcomere assembly. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein complexes.
Length = 58
Score = 34.0 bits (78), Expect = 0.017
Identities = 14/50 (28%), Positives = 22/50 (44%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C + ++ V G +WH+ CF C+ C +P F+ YC
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYC 50
Score = 29.7 bits (67), Expect = 0.50
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 2/58 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 335
C C + I ++ V G WH + F C+ C++P + K YC + + F
Sbjct: 1 CKGCYKDILAGDQNVEYKGNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
Score = 28.6 bits (64), Expect = 1.2
Identities = 9/24 (37%), Positives = 13/24 (54%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFY 148
G WH+ CF C+ C +P F+
Sbjct: 19 GNVWHKDCFTCSNCKQPIGTKSFF 42
Score = 27.0 bits (60), Expect = 5.2
Identities = 11/40 (27%), Positives = 18/40 (45%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 449
G WH + F C+ C++P + K YC + + F
Sbjct: 19 GNVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58
>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 = 33.9 bits (78), Expect = 0.017
Identities = 13/56 (23%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGG--IFYEFEGRKYCEHDF 61
C+ C++G P + + + +++H CF C C + G ++ E + C+ D+
Sbjct: 1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56
>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 = 33.5 bits (77), Expect = 0.018
Identities = 17/48 (35%), Positives = 22/48 (45%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C++ I VT + WH E FVC C+K G R + YC
Sbjct: 1 CAKCKKAITSGGVTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYC 48
Score = 30.0 bits (68), Expect = 0.31
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
WH +CF C C K+LA F C +C
Sbjct: 20 WHKECFVCTGCKKQLAGQRFTSRDEYPYCVDC 51
Score = 29.2 bits (66), Expect = 0.66
Identities = 11/31 (35%), Positives = 16/31 (51%)
Query: 27 ELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
+ WH++CFVC C + G F + YC
Sbjct: 18 QPWHKECFVCTGCKKQLAGQRFTSRDEYPYC 48
Score = 27.3 bits (61), Expect = 2.8
Identities = 12/29 (41%), Positives = 14/29 (48%)
Query: 413 WHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
WH E FVC C+K G R + YC
Sbjct: 20 WHKECFVCTGCKKQLAGQRFTSRDEYPYC 48
>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM
domains protein 2 (FHL2). The second LIM domain of
Four and a half LIM domains protein 2 (FHL2): FHL2 is
one of the best studied FHL proteins. FHL2 expression
is most abundant in the heart, and in brain, liver and
lung to a lesser extent. FHL2 participates in a wide
range of cellular processes, such as transcriptional
regulation, signal transduction, and cell survival by
binding to various protein partners. FHL2 has shown to
interact with more than 50 different proteins,
including receptors, structural proteins, transcription
factors and cofactors, signal transducers, splicing
factors, DNA replication and repair enzymes, and
metabolic enzymes. Although FHL2 is abundantly
expressed in heart, the fhl2 null mice are viable and
had no detectable abnormal cardiac phenotype. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to s
upport the assembly of multimeric protein complexes.
Length = 57
Score = 33.5 bits (76), Expect = 0.021
Identities = 14/50 (28%), Positives = 24/50 (48%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
CS C + P + + G WH+ CF+C +C +P F + + +C
Sbjct: 1 CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFC 50
Score = 27.3 bits (60), Expect = 3.8
Identities = 9/25 (36%), Positives = 15/25 (60%)
Query: 117 GEDRQTLTGGAWHQQCFVCAQCFRP 141
G + G +WH+ CF+C +C +P
Sbjct: 11 GTRKMEYKGNSWHETCFICQRCQQP 35
Score = 26.2 bits (57), Expect = 9.0
Identities = 11/41 (26%), Positives = 18/41 (43%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
R ++ +WH CF C+ C + + FI + C C
Sbjct: 13 RKMEYKGNSWHETCFICQRCQQPIGTKSFIPKDNQNFCVPC 53
>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP. The LIM domain of
N-RAP: N-RAP is a muscle-specific protein concentrated
at myotendinous junctions in skeletal muscle and
intercalated disks in cardiac muscle. LIM domain is
found at the N-terminus of N-RAP and the C-terminal of
N-RAP contains a region with multiple of nebulin
repeats. N-RAP functions as a scaffolding protein that
organizes alpha-actinin and actin into symmetrical
I-Z-I structures in developing myofibrils. Nebulin
repeat is known as actin binding domain. The N-RAP is
hypothesized to form antiparallel dimerization via its
LIM domain. As in other LIM domains, this domain family
is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 53
Score = 33.4 bits (76), Expect = 0.021
Identities = 18/51 (35%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C+RC G P EKI N + WH+ CF C C F + + YC+
Sbjct: 1 CARCGYGVYPAEKI-NCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50
Score = 29.5 bits (66), Expect = 0.47
Identities = 13/40 (32%), Positives = 17/40 (42%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHECN 199
I ++ WH CF CE C L F+ Q + C N
Sbjct: 14 INCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAHN 53
>gnl|CDD|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM
domains protein 1. The first LIM domain of Four and a
half LIM domains protein 1 (FHL1): FHL1 is heavily
expressed in skeletal and cardiac muscles. It plays
important roles in muscle growth, differentiation, and
sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes. .
Length = 54
Score = 33.2 bits (76), Expect = 0.022
Identities = 15/35 (42%), Positives = 19/35 (54%)
Query: 164 NANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
N WH CFRC C K LA+ F+ + LC +C
Sbjct: 19 NRYWHETCFRCAKCYKPLANEPFVAKDNKILCGKC 53
Score = 29.3 bits (66), Expect = 0.55
Identities = 13/51 (25%), Positives = 24/51 (47%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C+ C + + K ++ WH+ CF CA+C++P F + + C
Sbjct: 1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDNKILCG 51
Score = 29.0 bits (65), Expect = 0.79
Identities = 13/35 (37%), Positives = 20/35 (57%), Gaps = 2/35 (5%)
Query: 280 CGACRRPI--EERVVTALGKHWHVEHFVCARCEKP 312
C CR+PI + + + ++WH F CA+C KP
Sbjct: 1 CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKP 35
>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4. The second
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 = 56
Score = 33.5 bits (76), Expect = 0.025
Identities = 18/56 (32%), Positives = 27/56 (48%), Gaps = 2/56 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFP-GGIFYEFE-GRKYCEHDF 61
C+ C +G P + + + ++H CF C C R G FY E GR C+ D+
Sbjct: 1 CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56
Score = 26.9 bits (59), Expect = 4.7
Identities = 16/41 (39%), Positives = 23/41 (56%), Gaps = 2/41 (4%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELA--DLGFIRSQGRALCHE 197
V KA + +H CF C CS++LA D ++ GR +C E
Sbjct: 14 VRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKE 54
>gnl|CDD|188734 cd09348, LIM4_FHL1, The fourth LIM domain of Four and a half LIM
domains protein 1 (FHL1). The fourth LIM domain of Four
and a half LIM domains protein 1 (FHL1): FHL1 is
heavily expressed in skeletal and cardiac muscles. It
plays important roles in muscle growth, differentiation,
and sarcomere assembly by acting as a modulator of
transcription factors. Defects in FHL1 gene are
responsible for a number of Muscular dystrophy-like
muscle disorders. It has been detected that FHL1 binds
to Myosin-binding protein C, regulating myosin filament
formation and sarcomere assembly. LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 64
Score = 33.6 bits (77), Expect = 0.025
Identities = 13/32 (40%), Positives = 18/32 (56%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
WH CF C+ CS LA+ F+ G+ C +C
Sbjct: 29 WHDYCFNCKKCSLNLANKRFVFHNGQIYCSDC 60
Score = 30.1 bits (68), Expect = 0.42
Identities = 18/53 (33%), Positives = 21/53 (39%), Gaps = 3/53 (5%)
Query: 8 CSRCNE---GFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
CS C GF +VN G WH CF C +C F G+ YC
Sbjct: 5 CSGCQNPITGFGKGTNVVNYEGSSWHDYCFNCKKCSLNLANKRFVFHNGQIYC 57
>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 = 33.2 bits (76), Expect = 0.025
Identities = 14/35 (40%), Positives = 18/35 (51%)
Query: 164 NANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
N WH +CF C +CSK LA F + C +C
Sbjct: 17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADC 51
Score = 32.4 bits (74), Expect = 0.039
Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 12/55 (21%)
Query: 8 CSRCNEGFEPEEKIVNSNG-----ELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
CS+CN KI+NS G E WH++CF C C + G F + + YC
Sbjct: 1 CSKCN-------KIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
Score = 32.1 bits (73), Expect = 0.058
Identities = 16/48 (33%), Positives = 19/48 (39%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C + I VT + WH E F C C K G R + YC
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
Score = 26.7 bits (59), Expect = 5.0
Identities = 11/34 (32%), Positives = 19/34 (55%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTEL 245
C KC+ +I+ + ++ E +H F CT+C L
Sbjct: 1 CSKCNKIINSGGVTYKNEPWHRECFTCTNCSKSL 34
Score = 26.7 bits (59), Expect = 5.3
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 410 GKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
+ WH E F C C K G R + YC
Sbjct: 17 NEPWHRECFTCTNCSKSLAGQRFTSRDEKPYC 48
>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 = 32.9 bits (75), Expect = 0.028
Identities = 17/52 (32%), Positives = 27/52 (51%), Gaps = 1/52 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEH 59
C +C++ E+ V S G+ WH+ C C +C + G E +G+ YC H
Sbjct: 1 CPKCDKEVYFAER-VTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNH 51
Score = 28.3 bits (63), Expect = 1.3
Identities = 15/36 (41%), Positives = 17/36 (47%)
Query: 292 VTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
VT+LGK WH C +C K H E G YC
Sbjct: 14 VTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49
Score = 27.5 bits (61), Expect = 3.1
Identities = 10/37 (27%), Positives = 17/37 (45%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCH 196
+ ++ +WH C +CE C K L G+ C+
Sbjct: 14 VTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCN 50
Score = 26.0 bits (57), Expect = 8.8
Identities = 13/35 (37%), Positives = 16/35 (45%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
++LGK WH C +C K H E G YC
Sbjct: 15 TSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49
>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 = 33.1 bits (76), Expect = 0.030
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 280 CGACRRPIEERVVTALG-KHWHVEHFVCARCEKP 312
C C+ I E LG WH+ F C +C+K
Sbjct: 1 CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKK 34
Score = 28.9 bits (65), Expect = 1.0
Identities = 19/67 (28%), Positives = 26/67 (38%), Gaps = 14/67 (20%)
Query: 135 CAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKEL-ADLGF-IRSQGR 192
C C G YE G+ WH CF+C C K+L D F + G
Sbjct: 1 CVGCKESITEGHAYELGGDR------------WHIHCFKCYKCDKKLSCDSNFLVLGDGS 48
Query: 193 ALCHECN 199
+C +C+
Sbjct: 49 LICSDCS 55
Score = 28.1 bits (63), Expect = 1.6
Identities = 11/32 (34%), Positives = 13/32 (40%), Gaps = 1/32 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQC 39
C C E E G+ WH CF C +C
Sbjct: 1 CVGCKESIT-EGHAYELGGDRWHIHCFKCYKC 31
>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 = 33.2 bits (76), Expect = 0.032
Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 1/58 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFHVLF 65
C C + P EK V G +H+ CF C+ + EGR YC+H LF
Sbjct: 1 CVACGKTVYPIEK-VTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLF 57
>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 = 33.0 bits (75), Expect = 0.033
Identities = 14/32 (43%), Positives = 17/32 (53%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
WH CF C+ CS L GF+ + LC EC
Sbjct: 24 WHNDCFNCKKCSLSLVGRGFLTERDDILCPEC 55
>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 = 33.1 bits (75), Expect = 0.033
Identities = 20/53 (37%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 330
C C I+ +R + ALG WH FVCA C+ G Y KK C++H
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSH 53
Score = 32.7 bits (74), Expect = 0.042
Identities = 15/51 (29%), Positives = 24/51 (47%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C C+ + ++ + + G WH CFVCA C G FY + + C+
Sbjct: 1 CHGCDFKIDAGDRFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCK 51
Score = 28.9 bits (64), Expect = 0.88
Identities = 15/36 (41%), Positives = 18/36 (50%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 444
LG WH FVCA C+ G Y KK C++H
Sbjct: 18 LGFSWHDTCFVCAICQINLEGKTFYSKKDKPLCKSH 53
Score = 28.1 bits (62), Expect = 2.0
Identities = 12/38 (31%), Positives = 18/38 (47%)
Query: 158 RVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
R ++A+ +WH CF C C L F + + LC
Sbjct: 13 RFLEALGFSWHDTCFVCAICQINLEGKTFYSKKDKPLC 50
Score = 26.9 bits (59), Expect = 4.4
Identities = 12/24 (50%), Positives = 13/24 (54%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFY 148
G +WH CFVCA C G FY
Sbjct: 19 GFSWHDTCFVCAICQINLEGKTFY 42
>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx). The
second LIM domain of dLMO (Beaderx): dLMO is a nuclear
protein that plays important roles in transcriptional
regulation and development. In Drosophila dLMO
modulates the activity of LIM-homeodomain protein
Apterous (Ap), which regulates the formation of the
dorsal-ventral axis of the Drosophila wing. Biochemical
analysis shows that dLMO protein influences the
activity of Apterous by binding of its cofactor Chip.
Further studies shown that dLMO proteins might function
in an evolutionarily conserved mechanism involved in
patterning the appendages. All LIM domains are 50-60
amino acids in size and share two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 55
Score = 32.5 bits (74), Expect = 0.044
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 1/55 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPF-PGGIFYEFEGRKYCEHDF 61
C+ C++ E ++ + ++H +CF C +C F G FY E + CE+D+
Sbjct: 1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55
>gnl|CDD|188819 cd09435, LIM3_Zyxin, The third LIM domain of Zyxin. The third LIM
domain of Zyxin: Zyxin exhibits three copies of the LIM
domain, an extensive proline-rich domain and a nuclear
export signal. Localized at sites of cellsubstratum
adhesion in fibroblasts, Zyxin interacts with
alpha-actinin, members of the cysteine-rich protein
(CRP) family, proteins that display Src homology 3 (SH3)
domains and Ena/VASP family members. Zyxin and its
partners have been implicated in the spatial control of
actin filament assembly as well as in pathways important
for cell differentiation. In addition to its functions
at focal adhesion plaques, recent work has shown that
zyxin moves from the sites of cell contacts to the
nucleus, where it directly participates in the
regulation of gene expression. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 67
Score = 32.9 bits (75), Expect = 0.049
Identities = 25/74 (33%), Positives = 36/74 (48%), Gaps = 13/74 (17%)
Query: 132 CFVCAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELA----DLGFI 187
C VC++ P PG E V RV+ A+ N+H KC++CE C + L+ D G
Sbjct: 1 CCVCSEPIMPEPG------RDETV--RVV-ALEKNFHMKCYKCEDCGRPLSIEADDNGCF 51
Query: 188 RSQGRALCHECNAQ 201
G LC +C+
Sbjct: 52 PLDGHVLCMKCHTA 65
>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 = 32.2 bits (73), Expect = 0.058
Identities = 14/38 (36%), Positives = 21/38 (55%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
+ ++ NWH C +CE CSK L+ G G+ CH+
Sbjct: 14 VSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYCHK 51
Score = 30.7 bits (69), Expect = 0.21
Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 1/49 (2%)
Query: 280 CGACRRPIE-ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C + + V++LGK+WH C RC K H E G YC
Sbjct: 1 CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49
Score = 29.9 bits (67), Expect = 0.40
Identities = 18/50 (36%), Positives = 27/50 (54%), Gaps = 1/50 (2%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C RC++ EK V+S G+ WH+ C C +C + G E +G+ YC
Sbjct: 1 CPRCDKTVYFAEK-VSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49
Score = 28.4 bits (63), Expect = 1.2
Identities = 15/35 (42%), Positives = 17/35 (48%)
Query: 407 STLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
S+LGK+WH C RC K H E G YC
Sbjct: 15 SSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49
>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 = 31.8 bits (73), Expect = 0.063
Identities = 15/44 (34%), Positives = 23/44 (52%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
G+ G V++ + +H KCF C+ C +LA GF +G C
Sbjct: 5 GKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYC 48
Score = 27.2 bits (61), Expect = 3.0
Identities = 12/32 (37%), Positives = 15/32 (46%)
Query: 30 HQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
H +CF C C G F+ EG YC D+
Sbjct: 21 HIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52
Score = 26.1 bits (58), Expect = 9.0
Identities = 13/52 (25%), Positives = 22/52 (42%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + + V+ K++H++ F C C + K+G YC Y
Sbjct: 1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 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 = 32.0 bits (73), Expect = 0.066
Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 4/52 (7%)
Query: 280 CGACRRPI--EERVVTALGKHWHV--EHFVCARCEKPFLGHRHYEKKGLAYC 327
C C I ++ +T G+HWH + F CA+C+K LG K+G YC
Sbjct: 3 CDTCGEHIGVDQGQMTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYC 54
Score = 30.9 bits (70), Expect = 0.21
Identities = 15/34 (44%), Positives = 20/34 (58%), Gaps = 2/34 (5%)
Query: 410 GKHWHV--EHFVCARCEKPFLGHRHYEKKGLAYC 441
G+HWH + F CA+C+K LG K+G YC
Sbjct: 21 GQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYC 54
Score = 30.5 bits (69), Expect = 0.25
Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 7 YCSRCNEGFEPEEKIVNSNGELWH--QQCFVCAQCFRPFPGGIFYEFEGRKYC 57
YC C E ++ + +G+ WH ++CF CAQC + G F +G+ YC
Sbjct: 2 YCDTCGEHIGVDQGQMTYDGQHWHATEKCFCCAQCKKSLLGRPFLPKQGQIYC 54
>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 = 32.0 bits (73), Expect = 0.069
Identities = 16/50 (32%), Positives = 23/50 (46%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C E F K + G+ WH++CF C +C +P F + YC
Sbjct: 1 CDGCGEIFRAGMKKMEYKGQQWHEKCFCCCECKQPIGTKSFIPKDDDVYC 50
Score = 26.6 bits (59), Expect = 5.4
Identities = 11/32 (34%), Positives = 13/32 (40%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
WH KCF C C + + FI C C
Sbjct: 22 WHEKCFCCCECKQPIGTKSFIPKDDDVYCVPC 53
>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 = 31.8 bits (72), Expect = 0.070
Identities = 11/33 (33%), Positives = 19/33 (57%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELADLGFIRSQG 191
++K ++ +WH KC +C C +LA+ F R
Sbjct: 16 ILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDS 48
>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 = 32.0 bits (73), Expect = 0.083
Identities = 13/32 (40%), Positives = 15/32 (46%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
WH CF+C C + L D F LC EC
Sbjct: 26 WHEGCFKCFKCQRSLVDKPFAAKDEDLLCTEC 57
>gnl|CDD|188834 cd09450, LIM_ALP, This family represents the LIM domain of ALP,
actinin-associated LIM protein. This family represents
the LIM domain of ALP, actinin-associated LIM protein.
ALP contains an N-terminal PDZ domain, a C-terminal LIM
domain and an ALP-subfamily-specific 34-amino-acid motif
termed ALP-like motif (AM), which contains a putative
consensus protein kinase C (PKC) phosphorylation site
and two alpha-helices. ALP proteins are found in heart
and in skeletal muscle. ALP may act as a signaling
molecule which is regulated by PKC-dependent signaling.
ALP plays an essential role in the development of RV
(right ventricle) chamber. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 53
Score = 31.8 bits (72), Expect = 0.086
Identities = 15/44 (34%), Positives = 24/44 (54%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
G ++G V+KA + HP+CF C C+ L G+ +G+ C
Sbjct: 5 GSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYC 48
Score = 29.5 bits (66), Expect = 0.55
Identities = 18/51 (35%), Positives = 23/51 (45%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETH 330
C C I VV A K+ H E FVC+ C ++ +G YCE H
Sbjct: 1 CDKCGSGIVGTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCEAH 51
Score = 28.7 bits (64), Expect = 0.98
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C +C G +V + + H +CFVC+ C ++ EG+ YCE
Sbjct: 1 CDKCGSGIV--GTVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49
>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein
(TLP). The second LIM domain of thymus LIM protein
(TLP): TLP is the distant member of the CRP family of
proteins. TLP has two isomers (TLP-A and TLP-B) and
sharing approximately 30% with each of the three other
CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM
domains, connected by a flexible linker region. Unlike
the CRPs, TLP lacks the nuclear targeting signal
(K/R-K/R-Y-G-P-K) and is localized solely in the
cytoplasm. TLP is specifically expressed in the thymus
in a subset of cortical epithelial cells. TLP has a role
in development of normal thymus and in controlling the
development and differentiation of thymic epithelial
cells. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 54
Score = 31.5 bits (71), Expect = 0.093
Identities = 17/49 (34%), Positives = 23/49 (46%), Gaps = 1/49 (2%)
Query: 280 CGACRRPIE-ERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
C C +P+ V +LG++WH C RC+K H E G YC
Sbjct: 1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
Score = 30.0 bits (67), Expect = 0.35
Identities = 13/37 (35%), Positives = 17/37 (45%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCH 196
+ ++ NWH C RC+ C K L G G CH
Sbjct: 14 VMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYCH 50
Score = 29.6 bits (66), Expect = 0.53
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 408 TLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
+LG++WH C RC+K H E G YC
Sbjct: 16 SLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
Score = 28.4 bits (63), Expect = 1.2
Identities = 16/50 (32%), Positives = 23/50 (46%), Gaps = 1/50 (2%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C + EK++ S G WH+ C C +C + G E +G YC
Sbjct: 1 CPGCGKPVYFAEKVM-SLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49
>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 = 31.6 bits (72), Expect = 0.096
Identities = 14/54 (25%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPF-PGGIFYEFEGRKYCEHD 60
C++C + F + ++ + +++H +CF C+ C R PG F + +C+ D
Sbjct: 1 CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKAD 54
>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The second LIM
domain of Thyroid receptor-interacting protein 6
(TRIP6): TRIP6 is a member of the zyxin LIM protein
family and contains three LIM zinc-binding domains at
the C-terminal. TRIP6 protein localizes to focal
adhesion sites and along actin stress fibers.
Recruitment of this protein to the plasma membrane
occurs in a lysophosphatidic acid (LPA)-dependent
manner. TRIP6 recruits a number of molecules involved in
actin assembly, cell motility, survival and
transcriptional control. The function of TRIP6 in cell
motility is regulated by Src-dependent phosphorylation
at a Tyr residue. The phosphorylation activates the
coupling to the Crk SH2 domain, which is required for
the function of TRIP6 in promoting lysophosphatidic acid
(LPA)-induced cell migration. TRIP6 can shuttle to the
nucleus to serve as a coactivator of AP-1 and NF-kappaB
transcriptional factors. Moreover, TRIP6 can form a
ternary complex with the NHERF2 PDZ protein and LPA2
receptor to regulate LPA-induced activation of ERK and
AKT, rendering cells resistant to chemotherapy. Recent
evidence shows that TRIP6 antagonizes Fas-Induced
apoptosis by enhancing the antiapoptotic effect of LPA
in cells. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 31.4 bits (71), Expect = 0.10
Identities = 14/36 (38%), Positives = 19/36 (52%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPFLG 315
C C +PI ER++ A GK +H F C C + G
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDG 36
Score = 28.7 bits (64), Expect = 0.97
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 11 CNEGFEP-EEKIVNSNGELWHQQCFVCAQCFRPFPGGIF-YEFEGRKYCEHDF 61
C+ +P E+I+ + G+ +H CF C C R G F + G+ +C DF
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53
Score = 27.9 bits (62), Expect = 2.2
Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 13/52 (25%)
Query: 135 CAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGF 186
C+ C +P ++ R+++A +HP CF C C + L + F
Sbjct: 1 CSVCSKP-------------IMERILRATGKAYHPHCFTCVVCHRSLDGIPF 39
Score = 27.5 bits (61), Expect = 2.3
Identities = 12/35 (34%), Positives = 18/35 (51%)
Query: 212 CHKCHGLIDDKPLKFRGEVYHPYHFNCTSCGTELN 246
C C I ++ L+ G+ YHP+ F C C L+
Sbjct: 1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLD 35
Score = 26.8 bits (59), Expect = 5.8
Identities = 10/21 (47%), Positives = 11/21 (52%)
Query: 124 TGGAWHQQCFVCAQCFRPFPG 144
TG A+H CF C C R G
Sbjct: 16 TGKAYHPHCFTCVVCHRSLDG 36
>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 = 31.4 bits (71), Expect = 0.11
Identities = 21/61 (34%), Positives = 27/61 (44%), Gaps = 7/61 (11%)
Query: 135 CAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRAL 194
C QC R GG F +G A WHP+CF+C C + L DL + G+
Sbjct: 1 CQQCGRQICGGDIAVFASRAGLG-------ACWHPQCFQCASCQELLVDLIYFYQDGKIY 53
Query: 195 C 195
C
Sbjct: 54 C 54
Score = 31.0 bits (70), Expect = 0.21
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 26 GELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
G WH QCF CA C I++ +G+ YC
Sbjct: 23 GACWHPQCFQCASCQELLVDLIYFYQDGKIYC 54
Score = 29.5 bits (66), Expect = 0.72
Identities = 13/34 (38%), Positives = 17/34 (50%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEGEFVIGR 158
G WH QCF CA C I++ +G+ GR
Sbjct: 23 GACWHPQCFQCASCQELLVDLIYFYQDGKIYCGR 56
>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain
Kinase 2). The first LIM domain of LIMK2 (LIM domain
Kinase 2): LIMK2 is a member of the LIMK protein
family, which comprises LIMK1 and LIMK2. LIMK contains
two LIM domains, a PDZ domain, and a kinase domain.
LIMK is involved in the regulation of actin
polymerization and microtubule disassembly. LIMK
influences architecture of the actin cytoskeleton by
regulating the activity of the cofilin family proteins
cofilin1, cofilin2, and destrin. The mechanism of the
activation is to phosphorylates cofilin on serine 3 and
inactivates its actin-severing activity, altering the
rate of actin depolymerization. LIMK activity is
activated by phosphorylation of a threonine residue
within the activation loop of the kinase by
p21-activated kinases 1 and 4 and by Rho kinase. LIMKs
can function in both cytoplasm and nucleus. Both LIMK1
and LIMK2 can act in the nucleus to suppress
Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is
expressed in all tissues. While LIMK1 localizes mainly
at focal adhesions, LIMK2 is found in cytoplasmic
punctae, suggesting that they may have different
cellular functions. The activity of LIM kinase 2 to
regulate cofilin phosphorylation is inhibited by the
direct binding of Par-3. LIMK2 activation promotes cell
cycle progression. The phenotype of Limk2 knockout mice
shows a defect in spermatogenesis. The LIM domains have
been shown to play an important role in regulating
kinase activity and likely also contribute to LIMK
function by acting as sites of protein-to-protein
interactions. All LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein complexes.
Length = 53
Score = 31.4 bits (71), Expect = 0.12
Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 27 ELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
E WH CF C+ C +YE +G+ YC +
Sbjct: 19 EAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKHY 52
Score = 29.1 bits (65), Expect = 0.71
Identities = 14/40 (35%), Positives = 20/40 (50%), Gaps = 1/40 (2%)
Query: 292 VTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
+ + WH F C+ C+ L + +YEK G YC HY
Sbjct: 14 YRVVQEAWHNSCFQCSVCQDL-LTNWYYEKDGKLYCHKHY 52
Score = 29.1 bits (65), Expect = 0.80
Identities = 15/42 (35%), Positives = 21/42 (50%), Gaps = 1/42 (2%)
Query: 404 FACSTLGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
F + + WH F C+ C+ L + +YEK G YC HY
Sbjct: 12 FHYRVVQEAWHNSCFQCSVCQDL-LTNWYYEKDGKLYCHKHY 52
Score = 27.1 bits (60), Expect = 4.1
Identities = 10/37 (27%), Positives = 17/37 (45%), Gaps = 1/37 (2%)
Query: 161 KAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
+ + WH CF+C C L + + G+ CH+
Sbjct: 15 RVVQEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHK 50
>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9
family. The second LIM domain of Lhx2 and Lhx9 family:
Lhx2 and Lhx9 are highly homologous LHX regulatory
proteins. They belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
Although Lhx2 and Lhx9 are highly homologous, they
seems to play regulatory roles in different organs. In
animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. Lhx9 is expressed in several
regions of the developing mouse brain, the spinal cord,
the pancreas, in limb mesenchyme, and in the urogenital
region. Lhx9 plays critical roles in gonad development.
Homozygous mice lacking functional Lhx9 alleles
exhibit numerous urogenital defects, such as gonadal
agenesis, infertility, and undetectable levels of
testosterone and estradiol coupled with high FSH
levels. Lhx9 null mice are phenotypically female, even
those that are genotypically male. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 59
Score = 31.1 bits (71), Expect = 0.14
Identities = 17/55 (30%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGG-IFYEFEGRKYCEHDF 61
C+RC+ G E ++ + ++H CF CA C +P G F +G YC +
Sbjct: 5 CARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
Score = 30.3 bits (69), Expect = 0.35
Identities = 20/55 (36%), Positives = 25/55 (45%), Gaps = 3/55 (5%)
Query: 280 CGACRRPIE--ERVVTALGKHWHVEHFVCARCEKPFLGHRHY-EKKGLAYCETHY 331
C C I E V+ A +H+ F CA C KP H+ + GL YC HY
Sbjct: 5 CARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
Score = 27.6 bits (62), Expect = 2.7
Identities = 14/34 (41%), Positives = 18/34 (52%), Gaps = 1/34 (2%)
Query: 413 WHVEHFVCARCEKPFLGHRHY-EKKGLAYCETHY 445
+H+ F CA C KP H+ + GL YC HY
Sbjct: 26 FHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59
>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 = 30.7 bits (70), Expect = 0.18
Identities = 18/54 (33%), Positives = 32/54 (59%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+ C + P E++V ++G+L+H+ CF C+ C + G + EG+ YC+ F
Sbjct: 1 CAVCGKTVYPMERLV-ADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53
Score = 26.8 bits (60), Expect = 4.7
Identities = 14/49 (28%), Positives = 21/49 (42%), Gaps = 7/49 (14%)
Query: 148 YEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCH 196
Y E G++ +H CFRC HC+K L + +G+ C
Sbjct: 9 YPMERLVADGKL-------FHKSCFRCSHCNKTLRLGNYASLEGKLYCK 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 = 30.7 bits (69), Expect = 0.19
Identities = 16/50 (32%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C+RC + P EK VN + WH+ CF C C + ++ + YC
Sbjct: 1 CARCGKIVYPTEK-VNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYC 49
>gnl|CDD|153150 cd04878, ACT_AHAS, N-terminal ACT domain of the Escherichia coli
IlvH-like regulatory subunit of acetohydroxyacid
synthase (AHAS). ACT_AHAS: N-terminal ACT domain of the
Escherichia coli IlvH-like regulatory subunit of
acetohydroxyacid synthase (AHAS). AHAS catalyses the
first common step in the biosynthesis of the three
branched-chain amino acids. The first step involves the
condensation of either pyruvate or 2-ketobutyrate with
the two-carbon hydroxyethyl fragment derived from
another pyruvate molecule, covalently bound to the
coenzyme thiamine diphosphate. Bacterial AHASs generally
consist of regulatory and catalytic subunits. The
effector (valine) binding sites are proposed to be
located in two symmetrically related positions in the
interface between a pair of N-terminal ACT domains with
the C-terminal domain of IlvH contacting the catalytic
dimer. Plants Arabidopsis and Oryza have tandem IlvH
subunits; both the first and second ACT domain sequences
are present in this CD. Members of this CD belong to the
superfamily of ACT regulatory domains.
Length = 72
Score = 31.3 bits (72), Expect = 0.19
Identities = 14/56 (25%), Positives = 23/56 (41%), Gaps = 2/56 (3%)
Query: 460 HTISLHVSSREAVLSSDSSVFGLRHYEKKGLAYCETHYHQLFGNLCFVCN-QDHTI 514
HT+S+ V + VL+ S +F R + + L T + + V D I
Sbjct: 1 HTLSVLVENEPGVLNRISGLFARRGFNIESLTVGPTEDPGIS-RITIVVEGDDDVI 55
>gnl|CDD|188835 cd09451, LIM_RIL, The LIM domain of RIL. The LIM domain of RIL:
RIL contains an N-terminal PDZ domain, a LIM domain, and
a short consensus C-terminal region. It is the smallest
molecule in the ALP LIM domain containing protein
family. RIL was identified in rat fibroblasts and in
human lymphocytes. The LIM domain interacts with the
AMPA glutamate receptor in dendritic spines. The
consensus C-terminus interacts with PTP-BL, a
submembranous protein tyrosine phosphatase and the PDZ
domain is responsible to interact with alpha-actinin
molecules. LIM domains are 50-60 amino acids in size and
share two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 53
Score = 30.7 bits (69), Expect = 0.21
Identities = 13/44 (29%), Positives = 23/44 (52%)
Query: 152 GEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
G ++G ++KA + +HP+CF C+ C L G+ + C
Sbjct: 5 GNGIVGTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYC 48
Score = 29.1 bits (65), Expect = 0.79
Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 2/51 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C+RC G IV + +L+H +CF+C C ++ + + YCE
Sbjct: 1 CTRCGNGIV--GTIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYCE 49
>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function.
LIM domain in proteins of unknown function: LIM domains
are identified in a diverse group of proteins with wide
variety of biological functions, including gene
expression regulation, cell fate determination,
cytoskeleton organization, tumor formation, and
development. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes. They perform their functions through
interactions with other protein partners. The LIM
domains are 50-60 amino acids in size and share two
characteristic highly conserved zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. The consensus sequence of LIM
domain has been defined as
C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,
21)-C-x(2,3)-[CHD] (where X denotes any amino acid).
Length = 61
Score = 30.9 bits (70), Expect = 0.22
Identities = 17/50 (34%), Positives = 26/50 (52%), Gaps = 1/50 (2%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C+ C E+++ G+++H+ CF CA+C G FYE E YC
Sbjct: 5 CASCGLPVFLAERLLIE-GKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53
>gnl|CDD|188743 cd09357, LIM3_Zyxin_like, The third LIM domain of Zyxin-like
family. The third LIM domain of Zyxin like family: This
family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and
Trip6 LIM proteins. Members of Zyxin family contain
three tandem C-terminal LIM domains, and a proline-rich
N-terminal region. Zyxin proteins are detected
primarily in focal adhesion plaques. They function as
scaffolds, participating in the assembly of multiple
interactions and signal transduction networks, which
regulate cell adhesion, spreading, and motility. They
can also shuffle into nucleus. In nucleus, zyxin
proteins affect gene transcription by interaction with a
variety of nuclear proteins, including several
transcription factors, playing regulating roles in cell
proliferation, differentiation and apoptosis. As in
other LIM domains, this domain family is 50-60 amino
acids in size and shares two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 63
Score = 30.9 bits (70), Expect = 0.24
Identities = 13/44 (29%), Positives = 21/44 (47%), Gaps = 4/44 (9%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRS----QGRALCHECN 199
I A++ ++H C++CE C L+ + G LC CN
Sbjct: 20 IVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCKSCN 63
>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 = 30.8 bits (70), Expect = 0.25
Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 9/67 (13%)
Query: 135 CAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELADLGFIRS---QG 191
CA C +P EG RV+ +M+ ++H +C+ CE C +L D R G
Sbjct: 1 CAACGQPI-----LPAEGSEETIRVV-SMDKDYHVECYHCEDCGLQLNDEEGHRCYPLDG 54
Query: 192 RALCHEC 198
LCH C
Sbjct: 55 HLLCHSC 61
>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin.
The first LIM domain of protein LIMPETin: LIMPETin
contains 6 LIM domains at the C-terminal and an
N-terminal PET domain. Four of the six LIM domains are
highly homologous to the four and half LIM domain
protein family and two of them show sequence similarity
to the LIM domains of the Testin family. Thus, LIMPETin
may be the recombinant product of genes coding testin
and FHL proteins. In Schistosoma mansoni, where
LIMPETin was first identified, LIMPETin is down
regulated in sexually mature adult Schistosoma females
compared to sexually immature adult females and adult
male. Its differential expression indicates that it is a
transcription regulator. LIM domains are 50-60 amino
acids in size and share two characteristic zinc finger
motifs. The two zinc fingers contain eight conserved
residues, mostly cysteines and histidines, which
coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 30.4 bits (69), Expect = 0.26
Identities = 11/18 (61%), Positives = 12/18 (66%)
Query: 167 WHPKCFRCEHCSKELADL 184
WHP CFRC C + L DL
Sbjct: 26 WHPACFRCSTCEELLVDL 43
Score = 29.7 bits (67), Expect = 0.47
Identities = 19/58 (32%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 280 CGACRRPIE--ERVVTA----LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
CG C P++ E VTA WH F C+ CE+ + + YCE HY
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58
Score = 28.5 bits (64), Expect = 1.3
Identities = 12/36 (33%), Positives = 16/36 (44%), Gaps = 4/36 (11%)
Query: 8 CSRCNEGFEPEEKIVNS----NGELWHQQCFVCAQC 39
C C+E + E V + LWH CF C+ C
Sbjct: 1 CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTC 36
>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 = 30.2 bits (68), Expect = 0.27
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C C + P E++V +N +++H CF C+ C G + G YC+ F
Sbjct: 1 CVSCQKTVYPLERLV-ANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53
Score = 27.5 bits (61), Expect = 2.5
Identities = 9/29 (31%), Positives = 15/29 (51%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALC 195
+H CFRC +C+ +L+ + G C
Sbjct: 21 YHNSCFRCSYCNTKLSLGTYASLHGNIYC 49
>gnl|CDD|213834 TIGR03597, GTPase_YqeH, ribosome biogenesis GTPase YqeH. This
family describes YqeH, a member of a larger family of
GTPases involved in ribosome biogenesis. Like YqlF, it
shows a cyclical permutation relative to GTPases EngA
(in which the GTPase domain is duplicated), Era, and
others. Members of this protein family are found in a
relatively small number of bacterial species, including
Bacillus subtilis but not Escherichia coli [Protein
synthesis, Other].
Length = 360
Score = 33.0 bits (76), Expect = 0.37
Identities = 13/37 (35%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 238 CTSCGTELNSDAREVKSRPGYT---ANDMNELYCLRC 271
C CG + + +PGYT A + E+YC RC
Sbjct: 1 CIGCGAAIQTTD---PKKPGYTPKSALEKEEVYCQRC 34
>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM
domains protein 2 (FHL2). The first LIM domain of Four
and a half LIM domains protein 2 (FHL2): FHL2 is one of
the best studied FHL proteins. FHL2 expression is most
abundant in the heart, and in brain, liver and lung at
lesser extent. FHL2 participates in a wide range of
cellular processes, such as transcriptional regulation,
signal transduction, and cell survival by binding to
various protein partners. FHL2 has shown to interact
with more than 50 different proteins, including
receptors, structural proteins, transcription factors
and cofactors, signal transducers, splicing factors, DNA
replication and repair enzymes, and metabolic enzymes.
Although FHL2 is abundantly expressed in heart, the fhl2
null mice are viable and had no detectable abnormal
cardiac phenotype. LIM domains are 50-60 amino acids in
size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 62
Score = 30.3 bits (68), Expect = 0.38
Identities = 13/33 (39%), Positives = 15/33 (45%)
Query: 166 NWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
+WH CF C C L D F + LC EC
Sbjct: 25 HWHESCFHCFQCKNSLVDKPFAAKEEHLLCTEC 57
>gnl|CDD|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of
proteins with unknown function. This model represents
a LIM domain subfamily of Eplin-like family. This
family shows highest homology to the LIM domains on
Eplin and XIRP2 protein families. Epithelial Protein
Lost in Neoplasm is a cytoskeleton-associated tumor
suppressor whose expression inversely correlates with
cell growth, motility, invasion and cancer mortality.
Xirp2 is expressed in muscles and is an important
effector of the Ang II signaling pathway in the heart.
As in other LIM domains, this domain family is 50-60
amino acids in size and shares two characteristic zinc
finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 53
Score = 29.9 bits (67), Expect = 0.42
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
CS C + P E++V ++ ++H CF C C G + G YC+ F
Sbjct: 1 CSSCQKTVYPMERLV-ADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53
>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 = 29.9 bits (67), Expect = 0.42
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALC 195
WHP+CF C C++ L DL + G+ C
Sbjct: 26 WHPQCFVCSVCNELLVDLIYFYQDGKIYC 54
Score = 28.4 bits (63), Expect = 1.5
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 25 NGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
+G WH QCFVC+ C I++ +G+ YC
Sbjct: 22 HGVCWHPQCFVCSVCNELLVDLIYFYQDGKIYC 54
Score = 26.8 bits (59), Expect = 6.1
Identities = 13/34 (38%), Positives = 18/34 (52%)
Query: 125 GGAWHQQCFVCAQCFRPFPGGIFYEFEGEFVIGR 158
G WH QCFVC+ C I++ +G+ GR
Sbjct: 23 GVCWHPQCFVCSVCNELLVDLIYFYQDGKIYCGR 56
>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a. The first LIM
domain of Lhx3a: Lhx3a is a member of LHX protein
family, which features two tandem N-terminal LIM domains
and a C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. Lhx3a is one of
the two isoforms of Lhx3. The Lhx3 gene is expressed in
the ventral spinal cord, the pons, the medulla
oblongata, and the pineal gland of the developing
nervous system during mouse embryogenesis, and
transcripts are found in the emergent pituitary gland.
Lhx3 functions in concert with other transcription
factors to specify interneuron and motor neuron fates
during development. Lhx3 proteins have been demonstrated
to directly bind to the promoters of several pituitary
hormone gene promoters. The Lhx3 gene encodes two
isoforms, LHX3a and LHX3b that differ in their
amino-terminal sequences, where Lhx3a has longer
N-terminal. They show differential activation of
pituitary hormone genes and distinct DNA binding
properties. In human, Lhx3a trans-activated the
alpha-glycoprotein subunit promoter and genes containing
a high-affinity Lhx3 binding site more effectively than
the hLhx3b isoform. In addition, hLhx3a induce
transcription of the TSHbeta-subunit gene by acting on
pituitary POU domain factor, Pit-1, while hLhx3b does
not. As in other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 56
Score = 29.7 bits (67), Expect = 0.49
Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 1/39 (2%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
++K + WH KC +C C +L D F R G+ C E
Sbjct: 16 ILKVQDKPWHSKCLKCVDCQAQLTDKCFSRG-GQVYCKE 53
Score = 27.0 bits (60), Expect = 3.7
Identities = 16/53 (30%), Positives = 25/53 (47%), Gaps = 2/53 (3%)
Query: 277 IPICGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCE 328
IP C C PI +R ++ K WH + C C+ L + + + G YC+
Sbjct: 1 IPKCAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQ-LTDKCFSRGGQVYCK 52
>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 = 29.4 bits (66), Expect = 0.49
Identities = 15/50 (30%), Positives = 21/50 (42%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
C C + P + + G WH+ CFVC C +P E + YC
Sbjct: 1 CFHCKKTIMPGSRKLEFEGNEWHETCFVCQSCQQPIGTKPLITKENKNYC 50
Score = 27.1 bits (60), Expect = 4.3
Identities = 12/36 (33%), Positives = 17/36 (47%), Gaps = 1/36 (2%)
Query: 106 CFPLQRRFRARGEDRQTLTGGAWHQQCFVCAQCFRP 141
CF ++ G + G WH+ CFVC C +P
Sbjct: 1 CFHCKKTIMP-GSRKLEFEGNEWHETCFVCQSCQQP 35
>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 = 29.6 bits (67), Expect = 0.52
Identities = 17/43 (39%), Positives = 20/43 (46%), Gaps = 4/43 (9%)
Query: 160 IKAMNANWHPKCFRCEHCSKE----LADLGFIRSQGRALCHEC 198
IK + WH KCF C C +E L+D F R LC C
Sbjct: 13 IKFEDKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSNC 55
Score = 28.8 bits (65), Expect = 0.88
Identities = 11/32 (34%), Positives = 19/32 (59%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEK 311
C +C + IE+ + K WH++ F C+RC +
Sbjct: 1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHR 32
>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and
Lmx1b. The second LIM domain of Lmx1a and Lmx1b: Lmx1a
and Lmx1b belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as
transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs such as the pituitary gland and the pancreas.
Mouse Lmx1a is expressed in multiple tissues, including
the roof plate of the neural tube, the developing
brain, the otic vesicles, the notochord, and the
pancreas. In mouse, mutations in Lmx1a result in
failure of the roof plate to develop. Lmx1a may act
upstream of other roof plate markers such as MafB,
Gdf7, Bmp6, and Bmp7. Further characterization of these
mice reveals numerous defects including disorganized
cerebellum, hippocampus, and cortex; altered
pigmentation; female sterility, skeletal defects, and
behavioral abnormalities. In the mouse, Lmx1b
functions in the developing limbs and eyes, the
kidneys, the brain, and in cranial mesenchyme. The
disruption of Lmx1b gene results kidney and limb
defects. In the brain, Lmx1b is important for
generation of mesencephalic dopamine neurons and the
differentiation of serotonergic neurons. In the mouse
eye, Lmx1b regulates anterior segment (cornea, iris,
ciliary body, trabecular meshwork, and lens)
development. As in other LIM domains, this domain
family is 50-60 amino acids in size and shares two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to
support the assembly of multimeric protein.
Length = 55
Score = 29.7 bits (67), Expect = 0.52
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 1/55 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPF-PGGIFYEFEGRKYCEHDF 61
CS C E P E ++ + ++H +CF C C R G F EG+ C+ D+
Sbjct: 1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55
>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 = 29.6 bits (66), Expect = 0.54
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 1/39 (2%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
++K ++ +WH C +C C +LA+ F R+ G C E
Sbjct: 13 ILKVLDRHWHSSCLKCADCQMQLAERCFSRA-GNVYCKE 50
Score = 27.6 bits (61), Expect = 2.7
Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C + I ++ ++ L +HWH CA C+ L R + + G YC+ +
Sbjct: 1 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQ-LAERCFSRAGNVYCKEDF 52
Score = 26.9 bits (59), Expect = 4.6
Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+ CN+ ++ I+ WH C CA C F G YC+ DF
Sbjct: 1 CAGCNQHIL-DKFILKVLDRHWHSSCLKCADCQMQLAERCFSR-AGNVYCKEDF 52
>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 = 29.7 bits (67), Expect = 0.56
Identities = 24/74 (32%), Positives = 34/74 (45%), Gaps = 13/74 (17%)
Query: 132 CFVCAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHC----SKELADLGFI 187
C VC P PG + E V RV+ A++ ++H +C++CE C S E G
Sbjct: 1 CCVCKLPIMPEPG------QDETV--RVV-ALDRSFHVQCYKCEDCGLLLSSEAEGRGCY 51
Query: 188 RSQGRALCHECNAQ 201
LC CNA+
Sbjct: 52 PLDDHVLCKSCNAK 65
>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 = 29.4 bits (66), Expect = 0.64
Identities = 10/40 (25%), Positives = 22/40 (55%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
++ + + + CFRC CS+++ DL + +++ C C
Sbjct: 13 ILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRGLFCMSC 52
>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 = 29.2 bits (66), Expect = 0.67
Identities = 14/34 (41%), Positives = 20/34 (58%)
Query: 280 CGACRRPIEERVVTALGKHWHVEHFVCARCEKPF 313
C AC + I +V+ A GKH+H C+RC + F
Sbjct: 1 CEACDKFITGKVLEAGGKHYHPTCARCSRCGQMF 34
Score = 28.9 bits (65), Expect = 0.93
Identities = 10/30 (33%), Positives = 18/30 (60%)
Query: 154 FVIGRVIKAMNANWHPKCFRCEHCSKELAD 183
F+ G+V++A ++HP C RC C + +
Sbjct: 7 FITGKVLEAGGKHYHPTCARCSRCGQMFGE 36
>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 = 29.1 bits (65), Expect = 0.69
Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPF--LGHRHYEKKGLAYCETHY 331
C C R I++R ++ AL ++WH + CA C+ +G Y K L C Y
Sbjct: 1 CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55
>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 = 29.3 bits (65), Expect = 0.70
Identities = 11/39 (28%), Positives = 19/39 (48%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGG 46
C+RC+ G E ++ + ++H CF C C + G
Sbjct: 5 CARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTG 43
>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 = 29.1 bits (66), Expect = 0.72
Identities = 13/32 (40%), Positives = 16/32 (50%)
Query: 164 NANWHPKCFRCEHCSKELADLGFIRSQGRALC 195
A WHP CF C C + L DL + G+ C
Sbjct: 23 GACWHPACFVCSTCKELLVDLIYFYQDGKVYC 54
Score = 27.6 bits (62), Expect = 2.7
Identities = 11/29 (37%), Positives = 16/29 (55%)
Query: 29 WHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
WH CFVC+ C I++ +G+ YC
Sbjct: 26 WHPACFVCSTCKELLVDLIYFYQDGKVYC 54
>gnl|CDD|188820 cd09436, LIM3_TRIP6, The third LIM domain of Thyroid
receptor-interacting protein 6 (TRIP6). The third 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 = 66
Score = 29.6 bits (66), Expect = 0.76
Identities = 23/72 (31%), Positives = 34/72 (47%), Gaps = 12/72 (16%)
Query: 132 CFVCAQCFRPFPGGIFYEFEGEFVIGRVIKAMNANWHPKCFRCEHCSKELAD---LGFIR 188
C VC + P PG + E V I A++ ++H +C+RCE C L++ G
Sbjct: 1 CSVCKEPIMPAPG------QEETV---RIVALDRDFHVQCYRCEDCGSLLSEGDNQGCYP 51
Query: 189 SQGRALCHECNA 200
G LC CN+
Sbjct: 52 LDGHILCKACNS 63
>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 = 29.0 bits (65), Expect = 0.82
Identities = 14/37 (37%), Positives = 20/37 (54%), Gaps = 1/37 (2%)
Query: 25 NGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
N LWH++C CA C P FY + + YC+ D+
Sbjct: 17 NDSLWHERCLQCASCKEPLETTCFYR-DKKLYCKEDY 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 = 29.0 bits (65), Expect = 0.91
Identities = 12/34 (35%), Positives = 18/34 (52%)
Query: 294 ALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 327
A+ K WH HF C +C++ G R+ + YC
Sbjct: 18 AMNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYC 51
Score = 27.1 bits (60), Expect = 3.8
Identities = 11/33 (33%), Positives = 17/33 (51%)
Query: 409 LGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYC 441
+ K WH HF C +C++ G R+ + YC
Sbjct: 19 MNKDWHSGHFCCWQCDESLTGQRYVLRDEHPYC 51
>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 = 28.9 bits (64), Expect = 0.94
Identities = 17/56 (30%), Positives = 26/56 (46%), Gaps = 2/56 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFP-GGIFYEFE-GRKYCEHDF 61
C+ C +G P + + + ++H CF C C R G FY E R C+ D+
Sbjct: 2 CAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57
>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 = 28.7 bits (64), Expect = 0.98
Identities = 16/54 (29%), Positives = 26/54 (48%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRP-FPGGIFYEFEGRKYCEHD 60
C++C GF + ++ + ++H +CF C+ C R PG F E C D
Sbjct: 1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRAD 54
>gnl|CDD|188807 cd09423, LIM1_FHL3, The first LIM domain of Four and a half LIM
domains protein 3 (FHL3). The first LIM domain of Four
and a half LIM domains protein 3 (FHL3): FHL3 is highly
expressed in the skeleton and cardiac muscles and
possesses the transactivation and repression activities.
FHL3 interacts with many transcription factors, such as
CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3
interacts with alpha- and beta-subunits of the muscle
alpha7beta1 integrin receptor. FHL3 was also proved to
possess the auto-activation ability and was confirmed
that the second zinc finger motif in fourth LIM domain
was responsible for the auto-activation of FHL3. LIM
domains are 50-60 amino acids in size and share two
characteristic zinc finger motifs. The two zinc fingers
contain eight conserved residues, mostly cysteines and
histidines, which coordinately bond to two zinc atoms.
LIM domains function as adaptors or scaffolds to support
the assembly of multimeric protein complexes.
Length = 59
Score = 28.7 bits (64), Expect = 1.0
Identities = 13/33 (39%), Positives = 18/33 (54%)
Query: 166 NWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
++H CFRC C + LAD F LC++C
Sbjct: 25 HYHEHCFRCFRCDRSLADEPFTCQDEELLCNDC 57
>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4
family. The first LIM domain of Lhx3-Lhx4 family: Lhx3
and Lhx4 belong to the LHX protein family, which
features two tandem N-terminal LIM domains and a
C-terminal DNA binding homeodomain. Members of LHX
family are found in the nucleus and act as transcription
factors or cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs, such as
the pituitary gland and the pancreas. The LHX3 and LHX4
LIM-homeodomain transcription factors play essential
roles in pituitary gland and nervous system development.
Although LHX3 and LHX4 share marked sequence homology,
the genes have different expression patterns. They play
overlapping, but distinct functions during the
establishment of the specialized cells of the mammalian
pituitary gland and the nervous system. Lhx3 proteins
have been demonstrated the ability to directly bind to
the promoters/enhancers of several pituitary hormone
gene promoters to cause increased transcription. Lhx3a
and Lhx3b, whose mRNAs have distinct temporal expression
profiles during development, are two isoforms of Lhx3.
LHX4 plays essential roles in pituitary gland and
nervous system development. In mice, the lhx4 gene is
expressed in the developing hindbrain, cerebral cortex,
pituitary gland, and spinal cord. LHX4 shows significant
sequence similarity to LHX3, particularly to isoforms
Lhx3a. In gene regulation experiments, the LHX4 protein
exhibits regulation roles towards pituitary genes,
acting on their promoters/enhancers. As in other LIM
domains, this domain family is 50-60 amino acids in size
and shares two characteristic zinc finger motifs. The
two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 52
Score = 28.5 bits (64), Expect = 1.0
Identities = 13/39 (33%), Positives = 21/39 (53%), Gaps = 1/39 (2%)
Query: 159 VIKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
++K ++ WH KC +C C +L D F R+ G C +
Sbjct: 13 ILKVLDRTWHAKCLKCNDCGAQLTDKCFARN-GHVYCKD 50
>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1. The
first LIM domain of Prickle 1. Prickle contains three
C-terminal LIM domains and a N-terminal PET domain
Prickles have been implicated in roles of regulating
tissue polarity or planar cell polarity (PCP). PCP
establishment requires the conserved
Frizzled/Dishevelled PCP pathway. Prickle interacts with
Dishevelled, thereby modulating Frizzled/Dishevelled
activity and PCP signaling. Four forms of prickles have
been identified: prickle 1-4. The best characterized is
prickle 1 and prickle 2 which are differentially
expressed. While prickle 1 is expressed in fetal heart
and hematological malignancies, prickle 2 is found in
mainly expressed in fetal brain, adult cartilage,
pancreatic islet, and some types of timorous cells. In
addition, Prickle 1 regulates cell movements during
gastrulation and neuronal migration through interaction
with the noncanonical Wnt11/Wnt5 pathway in zebrafish.
Mutations in prickle 1 have been linked to progressive
myoclonus epilepsy. LIM domains are 50-60 amino acids
in size and share two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein
complexes.
Length = 59
Score = 28.7 bits (64), Expect = 1.0
Identities = 12/29 (41%), Positives = 16/29 (55%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALC 195
WHP CF C C++ L DL + G+ C
Sbjct: 26 WHPSCFVCFTCNELLVDLIYFYQDGKIHC 54
>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin. The first
LIM domain of Testin: Testin contains three C-terminal
LIM domains and a PET protein-protein interaction domain
at the N-terminal. Testin is a cytoskeleton associated
focal adhesion protein that localizes along actin stress
fibers, at cell-cell-contact areas, and at focal
adhesion plaques. Testin interacts with a variety of
cytoskeletal proteins, including zyxin, mena, VASP,
talin, and actin and it is involved in cell motility and
adhesion events. Knockout mice experiments reveal that
tumor repressor function of Testin. LIM domains are
50-60 amino acids in size and share two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein complexes.
Length = 58
Score = 28.6 bits (64), Expect = 1.1
Identities = 11/29 (37%), Positives = 15/29 (51%)
Query: 167 WHPKCFRCEHCSKELADLGFIRSQGRALC 195
WHP CF C C + L D+ + G+ C
Sbjct: 26 WHPACFVCSTCGELLVDMIYFWKNGKLYC 54
Score = 27.4 bits (61), Expect = 3.7
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 297 KHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
K WH FVC+ C + + ++ K G YC HY
Sbjct: 24 KLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58
Score = 27.4 bits (61), Expect = 3.7
Identities = 13/35 (37%), Positives = 18/35 (51%)
Query: 411 KHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 445
K WH FVC+ C + + ++ K G YC HY
Sbjct: 24 KLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58
Score = 26.3 bits (58), Expect = 8.3
Identities = 12/31 (38%), Positives = 17/31 (54%)
Query: 27 ELWHQQCFVCAQCFRPFPGGIFYEFEGRKYC 57
+LWH CFVC+ C I++ G+ YC
Sbjct: 24 KLWHPACFVCSTCGELLVDMIYFWKNGKLYC 54
>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 = 29.0 bits (65), Expect = 1.1
Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDFHVLF 65
C C++ +++ ++G ++H+ CF C+ C + EG YC+ F LF
Sbjct: 5 CKACDKTVYLVDQLS-ADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61
Score = 27.0 bits (60), Expect = 4.3
Identities = 16/59 (27%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 280 CGACRR---PIEERVVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHYHQLF 335
C AC + +++ ++A G +H F C+ C+ + +G+ YC+ H+ QLF
Sbjct: 5 CKACDKTVYLVDQ--LSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQLF 61
>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP).
The LIM domain of LIM and SH3 Protein (LASP): LASP
family contains two highly homologous members, LASP-1
and LASP-2. LASP contains a LIM motif at its amino
terminus, a src homology 3 (SH3) domains at its
C-terminal part, and a nebulin-like region in the
middle. LASP-1 and -2 are highly conserved in their
LIM, nebulin-like, and SH3 domains ,but differ
significantly at their linker regions. Both proteins
are ubiquitously expressed and involved in cytoskeletal
architecture, especially in the organization of focal
adhesions. LASP-1 and LASP-2, are important during
early embryo- and fetogenesis and are highly expressed
in the central nervous system of the adult. However,
only LASP-1 seems to participate significantly in
neuronal differentiation and plays an important
functional role in migration and proliferation of
certain cancer cells while the role of LASP-2 is more
structural. The expression of LASP-1 in breast tumors
is increased significantly. As in other LIM domains,
this domain family is 50-60 amino acids in size and
shares two characteristic zinc finger motifs. The two
zinc fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to
two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric
protein.
Length = 53
Score = 28.5 bits (64), Expect = 1.2
Identities = 15/51 (29%), Positives = 24/51 (47%), Gaps = 1/51 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCE 58
C+RC + P EK +N ++WH+ CF C C + + + YC
Sbjct: 1 CARCGKTVYPTEK-LNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCN 50
Score = 26.2 bits (58), Expect = 7.7
Identities = 8/15 (53%), Positives = 9/15 (60%)
Query: 167 WHPKCFRCEHCSKEL 181
WH CF+CE C L
Sbjct: 21 WHKGCFKCEVCGMTL 35
>gnl|CDD|220579 pfam10114, PocR, Sensory domain found in PocR. PocR, a ligand
binding domain, has a novel variant of the PAS-like
Fold. Evidence suggests that it binds small hydrocarbon
derivatives such as 1,3-propanediol.
Length = 173
Score = 30.6 bits (70), Expect = 1.2
Identities = 18/52 (34%), Positives = 25/52 (48%), Gaps = 12/52 (23%)
Query: 174 CEHCSKELADLGFIRS--QGRALCHECNAQAK--AVGFGKHMCHKCH-GLID 220
+ C F RS +GR C E +A+ AV GK ++CH GL+D
Sbjct: 42 QDFCR-------FHRSTPEGRKRCRESDAKLGREAVREGKPKIYRCHNGLVD 86
>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 = 28.1 bits (63), Expect = 1.5
Identities = 14/54 (25%), Positives = 22/54 (40%), Gaps = 2/54 (3%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLG-HRHYEKKGLAYCETHY 331
C C I++R + A+ + WH C C P + + G YC+ Y
Sbjct: 1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54
>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2. The second
LIM domain of Lhx2: Lhx2 belongs to the LHX protein
family, which features two tandem N-terminal LIM
domains and a C-terminal DNA binding homeodomain.
Members of LHX family are found in the nucleus and act
as transcription factors or cofactors. LHX proteins are
critical for the development of specialized cells in
multiple tissue types, including the nervous system,
skeletal muscle, the heart, the kidneys, and endocrine
organs, such as the pituitary gland and the pancreas.
In animals, Lhx2 plays important roles in eye, cerebral
cortex, limb, the olfactory organs, and erythrocyte
development. Lhx2 gene knockout mice exhibit impaired
patterning of the cortical hem and the telencephalon of
the developing brain, and a lack of development in
olfactory structures. The Lhx2 protein has been shown
to bind to the mouse M71 olfactory receptor promoter.
Similar to other LIM domains, this domain family is
50-60 amino acids in size and shares two characteristic
zinc finger motifs. The two zinc fingers contain eight
conserved residues, mostly cysteines and histidines,
which coordinately bond to two zinc atoms. LIM domains
function as adaptors or scaffolds to support the
assembly of multimeric protein.
Length = 59
Score = 28.5 bits (63), Expect = 1.6
Identities = 10/32 (31%), Positives = 17/32 (53%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQC 39
C+RC+ G E ++ + ++H CF C C
Sbjct: 5 CARCHLGISASEMVMRARDLVYHLNCFTCTTC 36
>gnl|CDD|173271 PRK14810, PRK14810, formamidopyrimidine-DNA glycosylase;
Provisional.
Length = 272
Score = 30.6 bits (69), Expect = 1.8
Identities = 13/42 (30%), Positives = 18/42 (42%), Gaps = 7/42 (16%)
Query: 270 RCHDKMGIPICGACRRPIEERVVTALGKHWHVEHFVCARCEK 311
R + + G P C C+ PI VV H+ C C+K
Sbjct: 238 RVYQRTGEP-CLNCKTPIRRVVVAGRSSHY------CPHCQK 272
>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 = 27.9 bits (62), Expect = 1.8
Identities = 17/55 (30%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPF--LGHRHYEKKGLAYCETHY 331
CG C++ I +R + A+ ++WH + C C +G R Y K G C Y
Sbjct: 1 CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 55
>gnl|CDD|224119 COG1198, PriA, Primosomal protein N' (replication factor Y) -
superfamily II helicase [DNA replication, recombination,
and repair].
Length = 730
Score = 31.1 bits (71), Expect = 1.8
Identities = 13/63 (20%), Positives = 21/63 (33%), Gaps = 14/63 (22%)
Query: 169 PKC---FRCEHCSKELADLGFIRSQGRALCHECNAQAKAVGFGKHMCHKCHGLIDDKPLK 225
C C +C + L ++ G+ CH C Q C +C + L+
Sbjct: 439 RDCGYIAECPNCD---SPLTLHKATGQLRCHYCGYQEPIP----QSCPECGS----EHLR 487
Query: 226 FRG 228
G
Sbjct: 488 AVG 490
>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 = 27.7 bits (62), Expect = 2.0
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIEERVVTALGKH-WHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C+RPI +R + + + WH E C+ C++P L Y + YC+ Y
Sbjct: 1 CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQP-LTTSCYFRDRKLYCKQDY 52
Score = 27.3 bits (61), Expect = 2.6
Identities = 10/41 (24%), Positives = 22/41 (53%), Gaps = 1/41 (2%)
Query: 21 IVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
++ N WH++C C+ C +P ++ + + YC+ D+
Sbjct: 13 LLRVNERSWHEECLQCSVCQQPLTTSCYFR-DRKLYCKQDY 52
>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 = 27.7 bits (62), Expect = 2.4
Identities = 15/54 (27%), Positives = 23/54 (42%), Gaps = 2/54 (3%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLGHRH-YEKKGLAYCETHY 331
C C PI +R ++ G+ WHV C C+ P + + YC+ Y
Sbjct: 1 CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 54
>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3
(LIM domain only protein 1 and 3). The second 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 = 27.3 bits (60), Expect = 3.1
Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)
Query: 280 CGACRR--PIEERVVTALGKHWHVEHFVCARCEKPF-LGHRHYEKKGLAYCETHY 331
C AC + P E V+ A +H++ F C C + F +G + + K + C+ Y
Sbjct: 1 CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55
>gnl|CDD|237511 PRK13796, PRK13796, GTPase YqeH; Provisional.
Length = 365
Score = 30.2 bits (69), Expect = 3.4
Identities = 13/41 (31%), Positives = 19/41 (46%), Gaps = 10/41 (24%)
Query: 238 CTSCGTELNSDAREVKSRPGYT-------ANDMNELYCLRC 271
C CG + + E K++PGY + E+YC RC
Sbjct: 3 CIGCGAAIQT---EDKNKPGYAPASALKKGLETEEVYCQRC 40
>gnl|CDD|234179 TIGR03355, VI_chp_2, type VI secretion protein, EvpB/VC_A0108
family. Work by Mougous, et al. (2006), describes
IAHP-related loci as a type VI secretion system
(PMID:16763151). This protein family is associated with
type VI secretion loci, although not treated explicitly
by Mougous, et al [Protein fate, Protein and peptide
secretion and trafficking, Cellular processes,
Pathogenesis].
Length = 473
Score = 30.3 bits (69), Expect = 3.5
Identities = 15/42 (35%), Positives = 17/42 (40%), Gaps = 9/42 (21%)
Query: 173 RCEHCSKELADLGFIRSQGRALCHECNAQAKAVGFGKHMCHK 214
R E ELA+LGFI L H N+ A F K
Sbjct: 321 RREF---ELAELGFI-----PLVHRKNSD-YAAFFSAQSVQK 353
>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 = 27.0 bits (60), Expect = 3.6
Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPFLGHRHYEKKGLAYCETHY 331
C C RPI ++ ++ L + WH + C C+ P L + + ++G YC +
Sbjct: 1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCP-LTEKCFSREGKLYCRNDF 52
>gnl|CDD|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL) like proteins. The LIM domain on proteins of
unknown function: This domain belongs to the LIM domain
family which are found on Mical (molecule interacting
with CasL)-like proteins. Known members of the
Mical-like family includes single LIM domain containing
proteins, Mical (molecule interacting with CasL), pollen
specific protein SF3, Eplin, xin actin-binding
repeat-containing protein 2 (XIRP2), and Ltd-1. The
members of this family function mainly at the
cytoskeleton and focal adhesions. They interact with
transcription factors or other signaling molecules to
play roles in muscle development, neuronal
differentiation, cell growth, and mobility. As in other
LIM domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately bond
to two zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 27.0 bits (60), Expect = 3.7
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 160 IKAMNANWHPKCFRCEHCSKEL 181
I A +H CFRC+ C+K+L
Sbjct: 14 IIAEKHIYHKNCFRCKDCNKQL 35
>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
Length = 679
Score = 30.1 bits (69), Expect = 3.7
Identities = 15/57 (26%), Positives = 16/57 (28%), Gaps = 11/57 (19%)
Query: 172 FRCEHCSKELADLGFIRSQGRALCHECNAQAKAVGFGKHMCHKCHGLIDDKPLKFRG 228
C HC L R Q R CH C Q C +C L G
Sbjct: 391 AECPHCDASLT---LHRFQRRLRCHHCGYQEPI----PKACPECGS----TDLVPVG 436
>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 = 27.0 bits (60), Expect = 3.9
Identities = 8/24 (33%), Positives = 14/24 (58%)
Query: 162 AMNANWHPKCFRCEHCSKELADLG 185
A++ WH C +C C +L ++G
Sbjct: 16 ALDRYWHNGCLKCSCCQAQLGEIG 39
Score = 26.2 bits (58), Expect = 8.1
Identities = 16/55 (29%), Positives = 26/55 (47%), Gaps = 3/55 (5%)
Query: 280 CGACRRPIEER-VVTALGKHWHVEHFVCARCEKPF--LGHRHYEKKGLAYCETHY 331
C C I +R ++ AL ++WH C+ C+ +G Y K G+ C+ Y
Sbjct: 1 CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55
>gnl|CDD|233829 TIGR02349, DnaJ_bact, chaperone protein DnaJ. This model
represents bacterial forms of DnaJ, part of the
DnaK-DnaJ-GrpE chaperone system. The three components
typically are encoded by consecutive genes. DnaJ
homologs occur in many genomes, typically not near DnaK
and GrpE-like genes; most such genes are not included by
this family. Eukaryotic (mitochondrial and chloroplast)
forms are not included in the scope of this family.
Length = 354
Score = 29.9 bits (68), Expect = 3.9
Identities = 10/34 (29%), Positives = 13/34 (38%), Gaps = 5/34 (14%)
Query: 184 LGFIRSQGRALCHECNAQAKAVGFGKHMCHKCHG 217
GF + Q C C + K + K C C G
Sbjct: 180 FGFFQQQ--QTCPTCGGEGKII---KEPCSTCKG 208
>gnl|CDD|148664 pfam07191, DUF1407, Protein of unknown function (DUF1407). This
family consists of several short, hypothetical bacterial
proteins of around 70 residues in length. Members of
this family have 8 highly conserved cysteine residues,
which form two zinc ribbon domains.
Length = 70
Score = 27.3 bits (61), Expect = 4.1
Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 192 RALCHECNAQA---KAVGFGKHMCHKCHGLIDDKPLKFR 227
+ALC +C+ + KA G + C+ C+ L K ++F
Sbjct: 30 QALCPDCHQELEVLKACGAVDYFCNHCNELKSKKRVEFE 68
>gnl|CDD|237666 PRK14296, PRK14296, chaperone protein DnaJ; Provisional.
Length = 372
Score = 29.9 bits (67), Expect = 4.1
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 3/35 (8%)
Query: 183 DLGFIRSQGRALCHECNAQAKAVGFGKHMCHKCHG 217
++GF + Q A C+ CN K + K+ C C G
Sbjct: 183 NMGFFQFQQSAKCNVCNGAGKII---KNKCKNCKG 214
>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost
in Neoplasm (Eplin) like proteins. The Lim domain of
Epithelial Protein Lost in Neoplasm (Eplin) like
proteins: This family contains Epithelial Protein Lost
in Neoplasm in Neoplasm (Eplin), xin actin-binding
repeat-containing protein 2 (XIRP2) and a group of
protein with unknown function. The members of this
family all contain a single LIM domain. Epithelial
Protein Lost in Neoplasm is a cytoskeleton-associated
tumor suppressor whose expression inversely correlates
with cell growth, motility, invasion and cancer
mortality. Eplin interacts and stabilizes F-actin
filaments and stress fibers, which correlates with its
ability to suppress anchorage independent growth. In
epithelial cells, Eplin is required for formation of the
F-actin adhesion belt by binding to the
E-cadherin-catenin complex through alpha-catenin. Eplin
is expressed in two isoforms, a longer Eplin-beta and a
shorter Eplin-alpha. Eplin-alpha mRNA is detected in
various tissues and cell lines, but is absent or down
regulated in cancer cells. Xirp2 contains a LIM domain
and Xin re peats for binding to and stabilising F-actin.
Xirp2 is expressed in muscles and is significantly
induced in the heart in response to systemic
administration of angiotensin II. Xirp2 is an important
effector of the Ang II signaling pathway in the heart.
The expression of Xirp2 is activated by myocyte enhancer
factor (MEF)2A, whose transcriptional activity is
stimulated by angiotersin II. Thus, Xirp2 plays
important pathological roles in the angiotensin II
induced hypertension. As in other LIM domains, this
domain family is 50-60 amino acids in size and shares
two characteristic zinc finger motifs. The two zinc
fingers contain eight conserved residues, mostly
cysteines and histidines, which coordinately bond to two
zinc atoms. LIM domains function as adaptors or
scaffolds to support the assembly of multimeric protein.
Length = 53
Score = 26.7 bits (59), Expect = 4.7
Identities = 13/30 (43%), Positives = 18/30 (60%)
Query: 166 NWHPKCFRCEHCSKELADLGFIRSQGRALC 195
N+H CFRCEHC+ +L+ + GR C
Sbjct: 20 NFHKSCFRCEHCNSKLSLGNYASLHGRIYC 49
Score = 26.3 bits (58), Expect = 7.8
Identities = 15/54 (27%), Positives = 27/54 (50%), Gaps = 1/54 (1%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGGIFYEFEGRKYCEHDF 61
C+ C + P E+++ ++ + +H+ CF C C G + GR YC+ F
Sbjct: 1 CTVCQKRVYPMERLI-ADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53
>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 = 27.1 bits (60), Expect = 4.9
Identities = 12/33 (36%), Positives = 13/33 (39%)
Query: 166 NWHPKCFRCEHCSKELADLGFIRSQGRALCHEC 198
+WH CF C C L D F R C C
Sbjct: 25 HWHEACFLCSKCKISLVDKPFGSKADRIYCGNC 57
Score = 26.0 bits (57), Expect = 9.6
Identities = 9/32 (28%), Positives = 19/32 (59%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQC 39
C C++ + K ++ + WH+ CF+C++C
Sbjct: 5 CEECSKIIGIDSKDLSYKDKHWHEACFLCSKC 36
>gnl|CDD|237653 PRK14276, PRK14276, chaperone protein DnaJ; Provisional.
Length = 380
Score = 29.3 bits (66), Expect = 5.5
Identities = 12/34 (35%), Positives = 15/34 (44%), Gaps = 5/34 (14%)
Query: 184 LGFIRSQGRALCHECNAQAKAVGFGKHMCHKCHG 217
LG +R Q C C+ K + K C CHG
Sbjct: 183 LGMMRRQ--VTCDVCHGTGKEI---KEPCQTCHG 211
Score = 29.3 bits (66), Expect = 5.9
Identities = 11/25 (44%), Positives = 11/25 (44%)
Query: 193 ALCHECNAQAKAVGFGKHMCHKCHG 217
A CH CN G C KCHG
Sbjct: 147 ATCHTCNGSGAKPGTSPVTCGKCHG 171
>gnl|CDD|193535 cd05659, M18_API, M18 Peptidase Aminopeptidase I. Peptidase M18
family, Aminopeptidase I (Vacuolar aminopeptidase I;
Polypeptidase; Leucine aminopeptidase IV; LAPIV;
Aminopeptidase III; Aminopeptidase yscI; EC 3.4.11.22)
subfamily. Aminopeptidase I is widely distributed in
bacteria and eukaryotes, but only the yeast enzyme has
been characterized to date. It is a vacuolar enzyme,
synthesized as a cytosolic proform, and proteolytically
matured upon arrival in the vacuole. The
pro-aminopeptidase I (proAPI) does not enter the vacuole
via the secretory pathway. In non-starved cells, it uses
the cytoplasm to vacuole targeting (cvt) pathway and in
cells starved for nitrogen, it is targeted to the
vacuole via autophagy. Yeast aminopeptidase I is active
only in its dodecameric form with broad substrate
specificity, acting on all aminoacyl and peptidyl
derivatives that contain a free alpha-amino group; this
is in contrast to the highly selective M18 mammalian
aspartyl aminopeptidase. N-terminal leucine and most
other hydrophobic amino acid residues are the best
substrates while glycine and charged amino acid residues
in P1 position are cleaved much more slowly. This enzyme
is strongly and specifically activated by zinc (Zn2+)
and chloride (Cl-) ions.
Length = 443
Score = 29.4 bits (67), Expect = 6.5
Identities = 8/14 (57%), Positives = 10/14 (71%)
Query: 537 YEKNGLAYCETHYH 550
YE GLA +THY+
Sbjct: 97 YEDEGLALLKTHYY 110
>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 = 26.2 bits (58), Expect = 6.9
Identities = 11/32 (34%), Positives = 17/32 (53%), Gaps = 1/32 (3%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQC 39
C RC + P E + +G +H+ CF C +C
Sbjct: 1 CPRCGKTAYPAESVDK-DGTFYHKGCFKCREC 31
>gnl|CDD|233040 TIGR00595, priA, primosomal protein N'. All proteins in this
family for which functions are known are components of
the primosome which is involved in replication, repair,
and recombination.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 505
Score = 29.3 bits (66), Expect = 7.3
Identities = 12/55 (21%), Positives = 21/55 (38%), Gaps = 11/55 (20%)
Query: 174 CEHCSKELADLGFIRSQGRALCHECNAQAKAVGFGKHMCHKCHGLIDDKPLKFRG 228
C +C L + + +G+ CH C Q C +C + L ++G
Sbjct: 225 CPNCD---VSLTYHKKEGKLRCHYCGYQEPI----PKTCPQCGS----EDLVYKG 268
>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8.
The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8
belong to the LHX protein family, which features two
tandem N-terminal LIM domains and a C-terminal DNA
binding homeodomain. Members of LHX family are found in
the nucleus and act as transcription factors or
cofactors. LHX proteins are critical for the
development of specialized cells in multiple tissue
types, including the nervous system, skeletal muscle,
the heart, the kidneys, and endocrine organs such as
the pituitary gland and the pancreas. Studies using
mutant mice have revealed roles for Lhx7 and Lhx8 in
the development of cholinergic neurons in the
telencephalon and in basal forebrain development. Mice
lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8
display dramatically reduced number of forebrain
cholinergic neurons. In addition, Lhx7 mutation affects
male and female mice differently, with females
appearing more affected than males. As in other LIM
domains, this domain family is 50-60 amino acids in
size and shares two characteristic zinc finger motifs.
The two zinc fingers contain eight conserved residues,
mostly cysteines and histidines, which coordinately
bond to two zinc atoms. LIM domains function as
adaptors or scaffolds to support the assembly of
multimeric protein.
Length = 55
Score = 26.2 bits (57), Expect = 7.6
Identities = 12/39 (30%), Positives = 17/39 (43%)
Query: 8 CSRCNEGFEPEEKIVNSNGELWHQQCFVCAQCFRPFPGG 46
CSRC + + + G ++H CF C C R G
Sbjct: 1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTG 39
>gnl|CDD|216058 pfam00684, DnaJ_CXXCXGXG, DnaJ central domain. The central
cysteine-rich (CR) domain of DnaJ proteins contains four
repeats of the motif CXXCXGXG where X is any amino acid.
The isolated cysteine rich domain folds in zinc
dependent fashion. Each set of two repeats binds one
unit of zinc. Although this domain has been implicated
in substrate binding, no evidence of specific
interaction between the isolated DNAJ cysteine rich
domain and various hydrophobic peptides has been found.
Length = 65
Score = 26.6 bits (59), Expect = 8.7
Identities = 8/33 (24%), Positives = 11/33 (33%), Gaps = 3/33 (9%)
Query: 185 GFIRSQGRALCHECNAQAKAVGFGKHMCHKCHG 217
Q + C +C K + K C C G
Sbjct: 34 PGGVFQMQQTCPKCGGTGKII---KDPCKVCKG 63
>gnl|CDD|181657 PRK09116, PRK09116, 3-oxoacyl-(acyl carrier protein) synthase II;
Reviewed.
Length = 405
Score = 28.8 bits (65), Expect = 9.1
Identities = 8/38 (21%), Positives = 12/38 (31%)
Query: 160 IKAMNANWHPKCFRCEHCSKELADLGFIRSQGRALCHE 197
I+ MN W L +I + R + E
Sbjct: 349 IEMMNEGWFAPTLNLTQVDPACGALDYIMGEAREIDTE 386
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 0.141 0.493
Gapped
Lambda K H
0.267 0.0693 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 29,452,673
Number of extensions: 2744582
Number of successful extensions: 4208
Number of sequences better than 10.0: 1
Number of HSP's gapped: 4074
Number of HSP's successfully gapped: 649
Length of query: 594
Length of database: 10,937,602
Length adjustment: 102
Effective length of query: 492
Effective length of database: 6,413,494
Effective search space: 3155439048
Effective search space used: 3155439048
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 (21.7 bits)
S2: 62 (27.7 bits)