Protein DA1; Proteins in this family include protein DA1 and its homologs. In Arabidopsis thaliana, DA1 is an ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation. It may act maternally to control seed mass.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751 321 GLNMKVEQEVPLLLVERQALNEAREGEKNGHYHMPETRGLCLSEEQTVSTVRKRSKHGTGKWAGN-ITEPYKLTRQCEVT 399
Cdd:pfam12315   1 GLNMKVEQEIPLLLVERQALNEAEEGEKIGHHHGPETRGLCLSEEQTVTSVLRRPRIGPGNRLVDmRTEPQRLTRRCEVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751 400 AILILFGLPRLLTGSILAHEMMHAWMRLKGFRTLSQDVEEGICQVMAHKWLDAELAAGSTNSNAASSSSSS------QGL 473
Cdd:pfam12315  81 AILVLYGLPRLLTGSILAHEMMHAWLRLNGYRNLNPEVEEGICQVLAHMWLESEIYAGSSATAASSSSSSSdsssssSSS 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1063684751 474 KKGPRSQYERKLGEFFKHQIESDASPVYGDGFRAGRLAVHKYGLRKTLEHIQMT 527
Cdd:pfam12315 161 KKGEKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANAAVNKYGLRRTLDHIRRT 214

membrane-attack complex/perforin (MACPF) Superfamily; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751  29 DNYPTASHDDEPSAADTDADNDEPHHTQEPSTSE----------DNTSNDQENEDIDRAIALS----LLEENQEQT-SIS 93
Cdd:PTZ00482  101 DEDDAGNATSGESSTDDDSLLELPDRDEDADTQAnndqtndfdqDDSSNSQTDQGLKQSVNLSsaekLIEEKKGQTeNTF 180

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1063684751  94 GKYSMPVDEDEQLARALQESMVVGNSPRHKSGSTYDNGN 132
Cdd:PTZ00482  181 KFYNFGNDGEEAAAKDGGKSKSSDPGPLNDSDGQGDDGD 219

Protein DA1; Proteins in this family include protein DA1 and its homologs. In Arabidopsis thaliana, DA1 is an ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation. It may act maternally to control seed mass.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751 321 GLNMKVEQEVPLLLVERQALNEAREGEKNGHYHMPETRGLCLSEEQTVSTVRKRSKHGTGKWAGN-ITEPYKLTRQCEVT 399
Cdd:pfam12315   1 GLNMKVEQEIPLLLVERQALNEAEEGEKIGHHHGPETRGLCLSEEQTVTSVLRRPRIGPGNRLVDmRTEPQRLTRRCEVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751 400 AILILFGLPRLLTGSILAHEMMHAWMRLKGFRTLSQDVEEGICQVMAHKWLDAELAAGSTNSNAASSSSSS------QGL 473
Cdd:pfam12315  81 AILVLYGLPRLLTGSILAHEMMHAWLRLNGYRNLNPEVEEGICQVLAHMWLESEIYAGSSATAASSSSSSSdsssssSSS 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1063684751 474 KKGPRSQYERKLGEFFKHQIESDASPVYGDGFRAGRLAVHKYGLRKTLEHIQMT 527
Cdd:pfam12315 161 KKGEKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANAAVNKYGLRRTLDHIRRT 214

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.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1063684751  171 ICAGCNMEI-GHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKAC 223
Cdd:smart00132   1 KCAGCGKPIyGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

membrane-attack complex/perforin (MACPF) Superfamily; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751  29 DNYPTASHDDEPSAADTDADNDEPHHTQEPSTSE----------DNTSNDQENEDIDRAIALS----LLEENQEQT-SIS 93
Cdd:PTZ00482  101 DEDDAGNATSGESSTDDDSLLELPDRDEDADTQAnndqtndfdqDDSSNSQTDQGLKQSVNLSsaekLIEEKKGQTeNTF 180

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1063684751  94 GKYSMPVDEDEQLARALQESMVVGNSPRHKSGSTYDNGN 132
Cdd:PTZ00482  181 KFYNFGNDGEEAAAKDGGKSKSSDPGPLNDSDGQGDDGD 219

Protein DA1; Proteins in this family include protein DA1 and its homologs. In Arabidopsis thaliana, DA1 is an ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation. It may act maternally to control seed mass.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751 321 GLNMKVEQEVPLLLVERQALNEAREGEKNGHYHMPETRGLCLSEEQTVSTVRKRSKHGTGKWAGN-ITEPYKLTRQCEVT 399
Cdd:pfam12315   1 GLNMKVEQEIPLLLVERQALNEAEEGEKIGHHHGPETRGLCLSEEQTVTSVLRRPRIGPGNRLVDmRTEPQRLTRRCEVT 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751 400 AILILFGLPRLLTGSILAHEMMHAWMRLKGFRTLSQDVEEGICQVMAHKWLDAELAAGSTNSNAASSSSSS------QGL 473
Cdd:pfam12315  81 AILVLYGLPRLLTGSILAHEMMHAWLRLNGYRNLNPEVEEGICQVLAHMWLESEIYAGSSATAASSSSSSSdsssssSSS 160

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1063684751 474 KKGPRSQYERKLGEFFKHQIESDASPVYGDGFRAGRLAVHKYGLRKTLEHIQMT 527
Cdd:pfam12315 161 KKGEKSQFEKKLGEFFKHQIETDTSPVYGDGFRAANAAVNKYGLRRTLDHIRRT 214

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).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063684751 172 CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACY 224
Cdd:cd08368     1 CAGCGKPIEGRELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

LIM domain; This family represents two copies of the LIM structural domain.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1063684751 172 CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISE-YEFSTSGNyPFHKACYRERY 228
Cdd:pfam00412   1 CAGCNRPIYDRELVRALGKVWHPECFRCAVCGKPLTTgDFYEKDGK-LYCKHDYYKLF 57

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1063684751 171 ICAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSG 215
Cdd:cd09462    21 VCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEKDG 65

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063684751 172 CAGCNMEIgHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACY 224
Cdd:cd09338     1 CGGCNKPI-LENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1063684751 172 CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSG 215
Cdd:cd09367     1 CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSREG 44

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1063684751 172 CAGCNmEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKAC 223
Cdd:cd09332     1 CGKCG-EFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063684751 172 CAGCNMEIGhGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACY 224
Cdd:cd09336     1 CAACNKPIV-GQVVTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1063684751 171 ICAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFS 212
Cdd:cd09467     3 LCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFS 44

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.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1063684751 172 CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPIS 207
Cdd:cd09370     1 CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLE 36

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1063684751 172 CAGCNMEIGHGrFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPF 219
Cdd:cd09410     1 CSGCGRPVKEN-YLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPL 47

membrane-attack complex/perforin (MACPF) Superfamily; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1063684751  29 DNYPTASHDDEPSAADTDADNDEPHHTQEPSTSE----------DNTSNDQENEDIDRAIALS----LLEENQEQT-SIS 93
Cdd:PTZ00482  101 DEDDAGNATSGESSTDDDSLLELPDRDEDADTQAnndqtndfdqDDSSNSQTDQGLKQSVNLSsaekLIEEKKGQTeNTF 180

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1063684751  94 GKYSMPVDEDEQLARALQESMVVGNSPRHKSGSTYDNGN 132
Cdd:PTZ00482  181 KFYNFGNDGEEAAAKDGGKSKSSDPGPLNDSDGQGDDGD 219

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063684751 172 CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACY 224
Cdd:cd09401     1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

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.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1063684751 190 SLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACYRERY 228
Cdd:cd09424    20 NVWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCHEKKF 58

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1063684751 172 CAGCNMEIGHgRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACY 224
Cdd:cd09337     1 CAYCNGPILD-KCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1063684751 172 CAGCNMEIGHG-RFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGN 216
Cdd:cd09344     1 CAECRKPIGADsKELHHKNRYWHETCFRCAKCYKPLANEPFVAKDN 46

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.

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gi 1063684751 172 CAGCNMEIGHG-RFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHK 221
Cdd:cd09363     1 CHGCDFPIEAGdRFLEALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCK 51

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.

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gi 1063684751 172 CAGCNMEIgHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYPFHKACY 224
Cdd:cd09457     1 CGRCQRKI-LGEVINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

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.

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gi 1063684751 172 CAGCNMEIgHGRFLNCLNSLWHPECFRCYGCSQPIseyefstsGNYPFH 220
Cdd:cd09362     1 CARCHKKI-LGEVMHALKQTWHVSCFVCAACKQPI--------GNSLFH 40

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.

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gi 1063684751 172 CAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPI 206
Cdd:cd09369     1 CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPL 35