NCBI Conserved Domain Search

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.

Pssm-ID: 188820 Cd Length: 66 Bit Score: 152.08 E-value: 2.27e-44

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 542 CSVCKEPIMPAPGQEETIRIVALDRDFHVQCYRCEDCGGLLSEGDNQGCYPLDGHILCKTCNSARI 607
Cdd:cd09436     1 CSVCKEPIMPAPGQEETVRIVALDRDFHVQCYRCEDCGSLLSEGDNQGCYPLDGHILCKACNSARI 66

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.

Pssm-ID: 188743 Cd Length: 63 Bit Score: 131.78 E-value: 5.41e-37

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 542 CSVCKEPIMPAPGQEETIRIVALDRDFHVQCYRCEDCGGLLS-EGDNQGCYPLDGHILCKTCN 603
Cdd:cd09357     1 CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSsEDEGQGCYPLDGHLLCKSCN 63

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.

Pssm-ID: 188821 Cd Length: 68 Bit Score: 124.12 E-value: 4.11e-34

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1820662107 542 CSVCKEPIMPAPGQEETIRIVALDRDFHVQCYRCEDCGGLL-SEGDNQGCYPLDGHILCKTCNSARIQ 608
Cdd:cd09437     1 CCVCKLPIMPEPGQDETVRVVALDRSFHVQCYKCEDCGLLLsSEAEGRGCYPLDDHVLCKSCNAKRVQ 68

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.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 120.20 E-value: 6.58e-33

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09350     1 CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

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.

Pssm-ID: 188742 Cd Length: 53 Bit Score: 117.28 E-value: 7.27e-32

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIHCIEDF 534
Cdd:cd09356     1 CSVCSKPIMERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53

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.

Pssm-ID: 188740 [Multi-domain] Cd Length: 60 Bit Score: 114.95 E-value: 6.22e-31

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIHCIEDFHKKFAPR 541
Cdd:cd09354     1 CSVCSKPILDRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKKFAPR 60

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.

Pssm-ID: 188819 Cd Length: 67 Bit Score: 107.65 E-value: 2.46e-28

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 542 CSVCKEPIMPAPGQEETIRIVALDRDFHVQCYRCEDCGGLLS-EGDNQGCYPLDGHILCKTCNSAR 606
Cdd:cd09435     1 CCVCSEPIMPEPGRDETVRVVALEKNFHMKCYKCEDCGRPLSiEADDNGCFPLDGHVLCMKCHTAR 66

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.

Pssm-ID: 188822 Cd Length: 62 Bit Score: 99.39 E-value: 1.68e-25

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                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 542 CSVCKEPIMPAPGQEETIRIVALDRDFHVQCYRCEDCGGLLSEGDNQGCYPLDGHILCKTC 602
Cdd:cd09438     1 CAACGQPILPAEGSEETIRVVSMDKDYHVECYHCEDCGLQLNDEEGHRCYPLDGHLLCHSC 61

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.

Pssm-ID: 188739 [Multi-domain] Cd Length: 60 Bit Score: 90.76 E-value: 1.80e-22

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                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIHCIEDFHKKFAPR 541
Cdd:cd09353     1 CAVCDQKITDRMLKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHRRYAPR 60

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.

Pssm-ID: 188737 [Multi-domain] Cd Length: 54 Bit Score: 85.17 E-value: 1.57e-20

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                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09351     1 CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYCEEDY 54

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.

Pssm-ID: 188741 [Multi-domain] Cd Length: 53 Bit Score: 84.32 E-value: 2.89e-20

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIHCIEDF 534
Cdd:cd09355     1 CAVCGHLIMEMILQALGKSYHPGCFRCCVCNECLDGVPFTVDVENNIYCVKDY 53

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.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 78.36 E-value: 1.03e-17

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 397 DELEHLTKKMLYDMENPPSDDYFGR--CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPC 474
Cdd:cd09349     7 EELEMLTQQLMQDMDHPPAAEAATNelCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQGQQFYSLEGKPYCEEC 86


                  .
gi 1820662107 475 Y 475
Cdd:cd09349    87 Y 87

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.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 72.42 E-value: 4.17e-16

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107  421 RCSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPC 474
Cdd:smart00132   1 KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 70.42 E-value: 2.21e-15

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEgTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd08368     1 CAGCGKPIEGR-ELLRALGKKWHPECFKCAECGKPLGGDSFYEKDGKPYCEKCY 53

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.

Pssm-ID: 188738 Cd Length: 54 Bit Score: 68.23 E-value: 1.59e-14

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09352     1 CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTLRGKAFYNVNGKVYCE 51

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).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 65.42 E-value: 1.37e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTVDaGGNIHCIEDF 534
Cdd:cd08368     1 CAGCGKPIEGReLLRALGKKWHPECFKCAECGKPLGGDSFYEK-DGKPYCEKCY 53

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.

Pssm-ID: 188758 [Multi-domain] Cd Length: 53 Bit Score: 63.21 E-value: 8.65e-13

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIHCIEDF 534
Cdd:cd09372     1 CAKCQGVITEHIIRALGKGYHPPCFTCVTCGRRIGDESFAVDEQNEVYCLDDY 53

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.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 62.02 E-value: 2.33e-12

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1820662107  541 RCSVCKEPIMPapgqeETIRIVALDRDFHVQCYRCEDCGGLLSegdNQGCYPLDGHILCKTC 602
Cdd:smart00132   1 KCAGCGKPIYG-----TERVLRALGKVWHPECFKCATCGKPLS---GDTFFEKDGKLYCKDC 54

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.

Pssm-ID: 214528 [Multi-domain] Cd Length: 54 Bit Score: 60.86 E-value: 4.71e-12

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107  482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDaGGNIHCIED 533
Cdd:smart00132   2 CAGCGKPIYgtERVLRALGKVWHPECFKCATCGKPLSGDTFFEK-DGKLYCKDC 54

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 59.27 E-value: 2.05e-11

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGENVVGEGTgCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCYIN 477
Cdd:pfam00412   1 CAGCNRPIYDREL-VRALGKVWHPECFRCAVCGKPLTTGDFYEKDGKLYCKHDYYK 55

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 56.19 E-value: 2.50e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSL-DGIPFTVDagGNIHCIEDFHKKF 538
Cdd:pfam00412   1 CAGCNRPIYDReLVRALGKVWHPECFRCAVCGKPLtTGDFYEKD--GKLYCKHDYYKLF 57

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).

Pssm-ID: 259829 [Multi-domain] Cd Length: 53 Bit Score: 55.02 E-value: 5.96e-10

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 542 CSVCKEPImpapgqEETIRIVALDRDFHVQCYRCEDCGGLLSEGDnqgCYPLDGHILCKTC 602
Cdd:cd08368     1 CAGCGKPI------EGRELLRALGKKWHPECFKCAECGKPLGGDS---FYEKDGKPYCEKC 52

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.

Pssm-ID: 188746 [Multi-domain] Cd Length: 52 Bit Score: 54.30 E-value: 9.40e-10

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGegTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09360     1 CDKCGNGIVG--VVVKARDKNRHPECFVCADCGLNLKNKGYFFIEDELYCE 49

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.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 52.78 E-value: 4.26e-09

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGtgCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09336     1 CAACNKPIVGQV--VTALGKTWHPEHFVCVHCQTELGTSNFFERDGKPYCEKDY 52

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

Pssm-ID: 395333 [Multi-domain] Cd Length: 57 Bit Score: 51.18 E-value: 1.71e-08

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 542 CSVCKEPImpapgqEETIRIVALDRDFHVQCYRCEDCGGLLSEGDNqgcYPLDGHILCKTC 602
Cdd:pfam00412   1 CAGCNRPI------YDRELVRALGKVWHPECFRCAVCGKPLTTGDF---YEKDGKLYCKHD 52

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.

Pssm-ID: 188732 Cd Length: 52 Bit Score: 50.79 E-value: 1.72e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09346     1 CAKCKKAITSGGV--TYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

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.

Pssm-ID: 188841 [Multi-domain] Cd Length: 52 Bit Score: 50.03 E-value: 3.08e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09457     1 CGRCQRKILGEVI--NALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

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.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 49.81 E-value: 3.74e-08

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1820662107 435 GCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09429    12 GVTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCY 52

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.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 49.61 E-value: 4.99e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09456     1 CAKCKKKITGEIM--HALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 52

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.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 49.48 E-value: 5.48e-08

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHCIEDFH 535
Cdd:cd09406     3 CASCQKPIAGQVVTALGQTWHPEHFVCCQCGKELGSRPF-FERNGQAYCEEDYH 55

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.

Pssm-ID: 188835 Cd Length: 53 Bit Score: 48.77 E-value: 1.07e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGegTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09451     1 CTRCGNGIVG--TIVKARDKLYHPECFMCDDCGLNLKQRGYFFIDEQLYCE 49

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.

Pssm-ID: 188748 [Multi-domain] Cd Length: 52 Bit Score: 48.24 E-value: 1.55e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09362     1 CARCHKKILGEVM--HALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

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.

Pssm-ID: 259830 [Multi-domain] Cd Length: 53 Bit Score: 48.15 E-value: 1.63e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHCIEDFH 535
Cdd:cd09336     1 CAACNKPIVGQVVTALGKTWHPEHFVCVHCQTELGTSNF-FERDGKPYCEKDYH 53

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.

Pssm-ID: 188773 Cd Length: 55 Bit Score: 47.86 E-value: 2.17e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAK--PIMERILRATGKAYHPHCFTCVMCHRSL-DGIPFTVdAGGNIHCIEDF 534
Cdd:cd09387     1 CSACGQsiPASELVMRAQGNVYHLKCFTCSTCHNQLvPGDRFHY-VNGSLFCEHDR 55

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.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 47.74 E-value: 2.57e-07

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHC 530
Cdd:cd09361     1 CAHCNQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGF-VEEKGSLYC 48

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.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 46.48 E-value: 5.75e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGEnVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09396     1 CAGCKS-EIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

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.

Pssm-ID: 188814 Cd Length: 52 Bit Score: 46.70 E-value: 5.91e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGEnVVGEGtGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09430     1 CSKCNK-IINSG-GVTYKNEPWHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

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.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 46.56 E-value: 7.54e-07

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSL-DGIPFTVDagGNIHCIEDFHKKFA 539
Cdd:cd09331     1 CERCREGFEpdEKIVNSNGELYHEQCFVCAQCFQPFpDGLFYEFE--GRKYCEHDFQVLFA 59

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.

Pssm-ID: 188773 Cd Length: 55 Bit Score: 46.32 E-value: 7.77e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKL-RGQPFYAVEKKAYCE 472
Cdd:cd09387     1 CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLvPGDRFHYVNGSLFCE 52

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.

Pssm-ID: 188790 [Multi-domain] Cd Length: 55 Bit Score: 46.40 E-value: 8.20e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 420 GRCSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09406     1 GDCASCQKPIAGQVV--TALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

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.

Pssm-ID: 188834 [Multi-domain] Cd Length: 53 Bit Score: 46.05 E-value: 8.91e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGegTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09450     1 CDKCGSGIVG--TVVKARDKYRHPECFVCSDCNLNLKQKGYFFVEGQLYCE 49

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.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 46.19 E-value: 9.33e-07

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVvgEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09334     3 CGACRRPI--EGRVVTALGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY 54

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 51.86 E-value: 1.19e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  150 TTSSPVTSPPGSTPVTGHKRMIIPnqPPLTATKKSTAKAPMQPAALPAPVPVTPVGTLKPqPQPVPASyiTASTPTRPaf 229
Cdd:PHA03247  2762 TTAGPPAPAPPAAPAAGPPRRLTR--PAVASLSESRESLPSPWDPADPPAAVLAPAAALP-PAASPAG--PLPPPTSA-- 2834

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  230 nVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAPqPARPPGPAQYVPSQPRGPDYGyAPQPARPSEPGYGYVPSQGRYQDL 309
Cdd:PHA03247  2835 -QPTAPPPPPGPPPPSLPLGGSVAPGGDVRRRP-PSRSPAAKPAAPARPPVRRLA-RPAVSRSTESFALPPDQPERPPQP 2911

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  310 YYPAGPGYGGRNGSEPSYVPQNTWKLEP---AYPTANTVAQNPPGTYQPPSTKKTYITDPVLAPPSPPMQPKSGYPASGS 386
Cdd:PHA03247  2912 QAPPPPQPQPQPPPPPQPQPPPPPPPRPqppLAPTTDPAGAGEPSGAVPQPWLGALVPGRVAVPRFRVPQPAPSREAPAS 2991


                   ....*
gi 1820662107  387 GSNAP 391
Cdd:PHA03247  2992 STPPL 2996

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 51.48 E-value: 1.72e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107   78 DDLGNLPAPPRAFPPPPSTDEAGFSVQVNPgektleerRSSLDAEIDSLTSILADLESSSPYKPRTQQGSGFTTSSPVTS 157
Cdd:PHA03247  2546 DDAGDPPPPLPPAAPPAAPDRSVPPPRPAP--------RPSEPAVTSRARRPDAPPQSARPRAPVDDRGDPRGPAPPSPL 2617

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  158 PPGSTPVTGHKRMIIPNQPPLTATKKSTAKAPMQPAALPAPVPVTPVGTLKPQPQPVPASYiTASTPTRPAFNVQV---- 233
Cdd:PHA03247  2618 PPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASS-PPQRPRRRAARPTVgslt 2696

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  234 ---------KTAQPSPHFQPPGPPPVQYGLGSNQSYAPQPARP-PGPAQYVPSQPRGPDYGYAPQ-PARPSEPGYGYVPS 302
Cdd:PHA03247  2697 sladpppppPTPEPAPHALVSATPLPPGPAAARQASPALPAAPaPPAVPAGPATPGGPARPARPPtTAGPPAPAPPAAPA 2776

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  303 QGRYQDLYYPAGPGYGGRNGSEPSYVPQNTWKLEPAYPTANTVAQNPPGTYQPPSTKKTYITDPVLAPPSPPMQPKSGYP 382
Cdd:PHA03247  2777 AGPPRRLTRPAVASLSESRESLPSPWDPADPPAAVLAPAAALPPAASPAGPLPPPTSAQPTAPPPPPGPPPPSLPLGGSV 2856


                   ...
gi 1820662107  383 ASG 385
Cdd:PHA03247  2857 APG 2859

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 51.24 E-value: 1.97e-06

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  193 AALPAPVPVTPVGTLKPQPQPVPASyitASTPTRPAFNVQVKTAQPSPHFQPPGPppVQYG----LGSNQSYAPQP--AR 266
Cdd:PRK10263   314 APITEPVAVAAAATTATQSWAAPVE---PVTQTPPVASVDVPPAQPTVAWQPVPG--PQTGepviAPAPEGYPQQSqyAQ 388

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  267 PPGPAQYVPSQPRGPDYGYAPQPAR--PSEPGYGYVPSQGRYQDLYYPAGPGYGGRNG-----SEPSYVPQNTWKLEPAY 339
Cdd:PRK10263   389 PAVQYNEPLQQPVQPQQPYYAPAAEqpAQQPYYAPAPEQPAQQPYYAPAPEQPVAGNAwqaeeQQSTFAPQSTYQTEQTY 468

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|.
gi 1820662107  340 PtaNTVAQNPPgTYQPPSTKKTYITDPV-----LAPPSPPM 375
Cdd:PRK10263   469 Q--QPAAQEPL-YQQPQPVEQQPVVEPEpvveeTKPARPPL 506

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.

Pssm-ID: 188763 Cd Length: 59 Bit Score: 44.96 E-value: 2.60e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 421 RCSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKA-YCEPCY 475
Cdd:cd09377     4 RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLvYCRLHY 59

chromosomal replication initiator protein DnaA;

Pssm-ID: 237605 [Multi-domain] Cd Length: 617 Bit Score: 49.82 E-value: 4.47e-06

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 199 VPVTPVGTLKPQPQPVPASYitaSTPTRPAFNVQVKTAQPSPHFQPPGPPPVQY-GLGSNQSYAPQPARPPGPAQYV-PS 276
Cdd:PRK14086   86 ITVDPSAGEPAPPPPHARRT---SEPELPRPGRRPYEGYGGPRADDRPPGLPRQdQLPTARPAYPAYQQRPEPGAWPrAA 162

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 277 QPRGPDY---GYAP--QPARPSEPGYGYVPSQGRYQDLYYPAGPGYGGRNGSEPSYVPQNTWKLE---PAyPTANTVAQN 348
Cdd:PRK14086  163 DDYGWQQqrlGFPPraPYASPASYAPEQERDREPYDAGRPEYDQRRRDYDHPRPDWDRPRRDRTDrpePP-PGAGHVHRG 241

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 1820662107 349 PPGTYQPPSTKKTYITDPvlAPPSPPMQPKsgyPASGSG 387
Cdd:PRK14086  242 GPGPPERDDAPVVPIRPS--APGPLAAQPA---PAPGPG 275

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.

Pssm-ID: 188727 Cd Length: 56 Bit Score: 43.36 E-value: 9.80e-06

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1820662107 421 RCSRCGENV-VGEgtgCT-AMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09341     2 RCAACDELIfSGE---YTqAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55

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.

Pssm-ID: 188789 [Multi-domain] Cd Length: 54 Bit Score: 43.07 E-value: 1.04e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHCIEDFH 535
Cdd:cd09405     2 CGACKKPIAGQVVTAMGKTWHPEHFVCTHCQEEIGSRNF-FERDGQPYCEKDYH 54

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.

Pssm-ID: 188815 Cd Length: 57 Bit Score: 43.06 E-value: 1.11e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1820662107 435 GCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCYIN 477
Cdd:cd09431    12 GVTYRDQPWHKECFVCTGCKKQLSGQRFTSRDDFAYCLNCFCN 54

translocon at the inner envelope of chloroplast subunit 62; Provisional

Pssm-ID: 178748 [Multi-domain] Cd Length: 576 Bit Score: 48.38 E-value: 1.15e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 177 PLTATKKSTAKAPMQ--------PAALPAPVPVTPVGTLKPQPQPVPASYITASTPTRP-----AFNVQVKTAQPSPHFQ 243
Cdd:PLN03209  312 PLTPMEELLAKIPSQrvppkesdAADGPKPVPTKPVTPEAPSPPIEEEPPQPKAVVPRPlspytAYEDLKPPTSPIPTPP 391

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 244 PPGPPPVQYGLGSNQSYAPQPARPPGPAQYVPSQPRGPDygyAPQPARPSEPgygYVpsqgRYQDLYYPAGPGYGGRNGS 323
Cdd:PLN03209  392 SSSPASSKSVDAVAKPAEPDVVPSPGSASNVPEVEPAQV---EAKKTRPLSP---YA----RYEDLKPPTSPSPTAPTGV 461

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 324 EPSYVPQNTWKLEP--AYPTANTVAQNPPGTYQPPSTKKTYITD------PVLAPPSPPMQPKSGYPASGSGSNAPLFRP 395
Cdd:PLN03209  462 SPSVSSTSSVPAVPdtAPATAATDAAAPPPANMRPLSPYAVYDDlkpptsPSPAAPVGKVAPSSTNEVVKVGNSAPPTAL 541

                         250       260
                  ....*....|....*....|....*...
gi 1820662107 396 EDELEHLTKK--------MLYDMENPPS 415
Cdd:PLN03209  542 ADEQHHAQPKprplspytMYEDLKPPTS 569

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.

Pssm-ID: 188762 Cd Length: 56 Bit Score: 43.11 E-value: 1.16e-05

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1820662107 482 CSVCAKPI--MERILRATGKAYHPHCFTCVMCHRSLD 516
Cdd:cd09376     1 CAGCDEGIppTQVVRRAQDNVYHLECFACFMCKRQLE 37

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 48.78 E-value: 1.21e-05

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107   30 GTPSISVSTQQTPKKFAPVVAPKPKYNPYKQPGIDDFPLPPPPPPLPGDDLGNLPAPPRAFPPPPSTDEAGFSVQVNPGE 109
Cdd:PHA03247  2602 VDDRGDPRGPAPPSPLPPDTHAPDPPPPSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQ 2681

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  110 KTleeRRSSLDAEIDSLTSiLADlessSPYKPRTQQGSGFTTSSPVTSPPGSTPVTGHkrmiiPNQPPLTATKKSTAKAP 189
Cdd:PHA03247  2682 RP---RRRAARPTVGSLTS-LAD----PPPPPPTPEPAPHALVSATPLPPGPAAARQA-----SPALPAAPAPPAVPAGP 2748

                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  190 MQPAAL-PAPVPVTPVGTLKPQPQPVPASYITASTPTRPAFNVQVKT-AQPSPHFQPPGPPPVQYGLGS-NQSYAPQPAR 266
Cdd:PHA03247  2749 ATPGGPaRPARPPTTAGPPAPAPPAAPAAGPPRRLTRPAVASLSESReSLPSPWDPADPPAAVLAPAAAlPPAASPAGPL 2828

                          250       260       270       280       290       300       310       320
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  267 PPgPAQYVPSQPRGPdygyaPQPARPSEPGYGYVPSQG----RYQDLYYPAGPGYGGRNGSEPSYVPQNTWKLEP-AYPT 341
Cdd:PHA03247  2829 PP-PTSAQPTAPPPP-----PGPPPPSLPLGGSVAPGGdvrrRPPSRSPAAKPAAPARPPVRRLARPAVSRSTESfALPP 2902

                          330       340       350       360       370
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107  342 ANTVAQNPPGTYQPPSTKKTYITDPVLAPPsPPMQPKSGYPASGSGSNAPLFRPE 396
Cdd:PHA03247  2903 DQPERPPQPQAPPPPQPQPQPPPPPQPQPP-PPPPPRPQPPLAPTTDPAGAGEPS 2956

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.

Pssm-ID: 188713 [Multi-domain] Cd Length: 52 Bit Score: 42.63 E-value: 1.54e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVdAGGNIHCIEDF 534
Cdd:cd09327     1 CYKCGKKCKGEVLRVQDKYFHIKCFTCKVCGCDLAQGGFFV-KEGEYYCTDDY 52

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 47.95 E-value: 1.69e-05

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 142 RTQQGSGFTTSSPVTSPPGSTPVtghkrmiiPNQPPLTATKKSTAKAPMQPAALPAPVPVTPVGTLKPQPQPVPASYITA 221
Cdd:PRK12323  364 RPGQSGGGAGPATAAAAPVAQPA--------PAAAAPAAAAPAPAAPPAAPAAAPAAAAAARAVAAAPARRSPAPEALAA 435

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 222 STPTRPAFNVQVKTAQPSPhfqppgpppvqyglgsnqSYAPQPARPPGPAQYVPSQPRGPDYGYAPQPARPSEPGYGYVP 301
Cdd:PRK12323  436 ARQASARGPGGAPAPAPAP------------------AAAPAAAARPAAAGPRPVAAAAAAAPARAAPAAAPAPADDDPP 497

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 302 SQGRYQDLYYPAGPgyggrngsepsyvpqntWKLEPAYPTANTVAQNPPGTYQPPSTKKTYITDPVLAPPSPPMQPKSGY 381
Cdd:PRK12323  498 PWEELPPEFASPAP-----------------AQPDAAPAGWVAESIPDPATADPDDAFETLAPAPAAAPAPRAAAATEPV 560


                  ....*....
gi 1820662107 382 PASGSGSNA 390
Cdd:PRK12323  561 VAPRPPRAS 569

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.

Pssm-ID: 188850 [Multi-domain] Cd Length: 56 Bit Score: 42.07 E-value: 2.18e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 540 PRCSVCKEPIMpapgqeETIRIVALDRDFHVQCYRCEDCGGLLSEgdnqGCYPLDGHILCK 600
Cdd:cd09466     2 PKCAGCDHPIF------DRFILKVQDKPWHSKCLKCVDCQAQLTD----KCFSRGGQVYCK 52

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.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 42.29 E-value: 2.30e-05

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHR 513
Cdd:cd09391     1 CAKCGKPITGQFVRALGDVYHLDCFTCHDCGK 32

This family represents the LIM domain of CLP36; This family represents the LIM domain of CLP36. CLP36 has also been named as CLIM1, Elfin, or PDLIM1. CLP36 contains a C-terminal LIM domain and an N-terminal PDZ domain. CLP36 is highly expressed in heart and is present in many other tissues including lung, liver, spleen, and blood. CLP36 has been implicated in many processes including hypoxia and regulation of actin stress fibers. CLP36 co-localizes with alpha-actinin-2 at the Z-lines in myocardium. In addition, CLP36 binds to alpha-actinin-1 and alpha-actinin-4, and associates with F-actin filaments and stress fibers. CLP36 might be involved in not only the function of sarcomeres in muscle cells, but also in actin stress fiber-mediated cellular processes, such as cell shape, migration, polarit, and cytokinesis in non-muscle cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188832 Cd Length: 52 Bit Score: 41.83 E-value: 2.93e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGegTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09448     1 CDKCGSGIVG--VFVKIRDKPRHPECYVCTDCGTNLKQKGHFFVEDQIYCE 49

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.

Pssm-ID: 188755 [Multi-domain] Cd Length: 54 Bit Score: 41.56 E-value: 3.33e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIHCIEDF 534
Cdd:cd09369     1 CAGCGEKIQDRfYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 54

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.

Pssm-ID: 188759 [Multi-domain] Cd Length: 54 Bit Score: 41.21 E-value: 4.19e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIP--FTVDagGNIHCIEDF 534
Cdd:cd09373     1 CTGCGEPITDRfLLKVSGRSWHVSCLRCCVCQTPLERQPscFTRD--RQIYCKADY 54

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.

Pssm-ID: 188850 [Multi-domain] Cd Length: 56 Bit Score: 41.30 E-value: 4.29e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTvdAGGNIHCIEDF 534
Cdd:cd09466     4 CAGCDHPIFDRfILKVQDKPWHSKCLKCVDCQAQLTDKCFS--RGGQVYCKEDF 55

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.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 41.12 E-value: 5.58e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHC 530
Cdd:cd09454     1 CGHCNNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSF-VEEQNNVYC 48

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.

Pssm-ID: 188762 Cd Length: 56 Bit Score: 41.18 E-value: 5.62e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLR-GQPFYAVE-KKAYCEPCY 475
Cdd:cd09376     1 CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLEtGDEFYLMEdDRLVCKKDY 56

The second LIM domain of Arrowhead (AWH); The second 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.

Pssm-ID: 188765 Cd Length: 55 Bit Score: 40.87 E-value: 5.81e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLR-GQPFYAVEKKAYCEPCY 475
Cdd:cd09379     1 CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLStGEEFALIEDRVLCKAHY 55

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.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 40.88 E-value: 5.96e-05

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1820662107 438 AMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYC 471
Cdd:cd09363    17 ALGHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLC 50

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.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 40.77 E-value: 6.27e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGEnVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQpFYAVEKKAYCEPCY 475
Cdd:cd09329     1 CAGCGQ-EIKNGQALLALDKQWHVWCFKCKECGKVLTGE-YMGKDGKPYCERDY 52

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.

Pssm-ID: 188836 [Multi-domain] Cd Length: 52 Bit Score: 40.94 E-value: 6.71e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHC 530
Cdd:cd09452     1 CAQCNKIIRGRYLVALGRSYHPEEFTCSQCKKVLDEGGF-FEEKGSIFC 48

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.

Pssm-ID: 188714 Cd Length: 56 Bit Score: 40.79 E-value: 7.65e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 421 RCSRCGENVVGEGTgcTAMDQVFHVECFTCVTCgnklrGQPFYAVEKKAY------CEPC 474
Cdd:cd09328     3 KCDSCQDFVEGEVV--SALGKTYHPKCFVCSVC-----RQPFPPGDRVTFngkeclCQKC 55

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.

Pssm-ID: 188753 [Multi-domain] Cd Length: 52 Bit Score: 40.49 E-value: 7.89e-05

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 542 CSVCKEPIMpapgqeETIRIVALDRDFHVQCYRCEDCGGLLSEgdnqGCYPLDGHILCKT 601
Cdd:cd09367     1 CAGCDRPIL------DKFLLNVLDRAWHAKCVQCCDCKCPLTE----KCFSREGKLYCRN 50

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.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 40.40 E-value: 8.92e-05

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAG 525
Cdd:cd09332     1 CGKCGEFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAG 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.

Pssm-ID: 188718 [Multi-domain] Cd Length: 52 Bit Score: 40.40 E-value: 9.46e-05

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPC 474
Cdd:cd09332     1 CGKCGEFVIGRVI--KAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

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.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 40.36 E-value: 1.04e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1820662107 542 CSVCKEPImpaPGQeeTIRivALDRDFHVQCYRCEDCGGLLS-------EGDNQGCYPL 593
Cdd:cd09391     1 CAKCGKPI---TGQ--FVR--ALGDVYHLDCFTCHDCGKPVAskffpvdDPDTSEQVPL 52

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.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 40.01 E-value: 1.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVVGegtGC-TAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09339     1 CAGCGKPITG---RCiTAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

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.

Pssm-ID: 188717 Cd Length: 59 Bit Score: 40.39 E-value: 1.17e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 422 CSRCG------ENVVGEGtgctamDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09331     1 CERCRegfepdEKIVNSN------GELYHEQCFVCAQCFQPFPDGLFYEFEGRKYCEHDF 54

The LIM domains of Cysteine Rich Protein (CRP) family; The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188712 Cd Length: 53 Bit Score: 39.89 E-value: 1.23e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1820662107 482 CSVCAKPIM--ERILrATGKAYHPHCFTCVMCHRSLD 516
Cdd:cd09326     1 CPRCGKSVYaaEEVI-AAGKSWHKSCFTCAVCNKRLD 36

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.

Pssm-ID: 188713 [Multi-domain] Cd Length: 52 Bit Score: 39.93 E-value: 1.23e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09327     1 CYKCGKKCKGEVL--RVQDKYFHIKCFTCKVCGCDLAQGGFFVKEGEYYCTDDY 52

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.

Pssm-ID: 188769 Cd Length: 55 Bit Score: 40.02 E-value: 1.31e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLR-GQPFYAVEKKAYC 471
Cdd:cd09383     1 CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLStGEEFALVEEKVLC 51

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237864 [Multi-domain] Cd Length: 585 Bit Score: 44.80 E-value: 1.40e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 156 TSPPGSTP--VTGHKRMIIPNQPPLTATKKSTAKAPMQPAALPAPVPVTPVGTLKPQPQPVPASYITASTPTRPAfnvqv 233
Cdd:PRK14950  343 TTSYGQLPleLAVIEALLVPVPAPQPAKPTAAAPSPVRPTPAPSTRPKAAAAANIPPKEPVRETATPPPVPPRPV----- 417

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 234 ktAQPSPHfqppgpppvqyglgsnqsyaPQPARPPGPAQYVPSQPRGPdygyAPQPARPSE 294
Cdd:PRK14950  418 --APPVPH--------------------TPESAPKLTRAAIPVDEKPK----YTPPAPPKE 452

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.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 39.63 E-value: 1.48e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRS--------LDGIPF 520
Cdd:cd09338     1 CGGCNKPILENYISALNTQWHPECFVCRECHKPfingsffeHEGLPY 47

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.

Pssm-ID: 188831 Cd Length: 53 Bit Score: 39.67 E-value: 1.50e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVVG-EGTGCtaMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09447     1 CARCGKTVYPtEKLNC--LDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 53

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.

Pssm-ID: 188738 Cd Length: 54 Bit Score: 39.72 E-value: 1.50e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 482 CSVCAKPI--MERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHCIEDF 534
Cdd:cd09352     1 CVKCGKGVygASQACQAMGNLYHTNCFTCCSCGRTLRGKAF-YNVNGKVYCEEDY 54

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.

Pssm-ID: 188754 Cd Length: 52 Bit Score: 39.71 E-value: 1.63e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1820662107 542 CSVCKEPIMpapgqeETIRIVALDRDFHVQCYRCEDCGGLLSEgdnqGCYPLDGHILCK 600
Cdd:cd09368     1 CGGCQEHIL------DRFILKVLDRTWHAKCLKCNDCGAQLTD----KCFARNGHVYCK 49

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.

Pssm-ID: 188764 Cd Length: 55 Bit Score: 39.74 E-value: 1.64e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLD-GIPFTVDAgGNIHCIEDF 534
Cdd:cd09378     1 CSGCLEKIApsELVMRALENVYHLRCFCCCVCERQLQkGDEFVLKE-GQLLCKSDY 55

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.

Pssm-ID: 188871 [Multi-domain] Cd Length: 54 Bit Score: 39.71 E-value: 1.71e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAmDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09840     1 CSRCGDSVYAAEKIMGA-GKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCY 53

DNA translocase FtsK; Provisional

Pssm-ID: 236669 [Multi-domain] Cd Length: 1355 Bit Score: 44.69 E-value: 1.84e-04

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  207 LKPQPQPVPASYITASTPTRPAFNVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAPQPARP---PGPAQYVP----SQPR 279
Cdd:PRK10263   311 LNGAPITEPVAVAAAATTATQSWAAPVEPVTQTPPVASVDVPPAQPTVAWQPVPGPQTGEPviaPAPEGYPQqsqyAQPA 390

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  280 GPDYGYAPQPARPSEPGYGYVPSQGRYQDLYYPAGPGYGGRNGSEPSY---VPQNTWKLEPA-YPTANTVAQNPPGTYQP 355
Cdd:PRK10263   391 VQYNEPLQQPVQPQQPYYAPAAEQPAQQPYYAPAPEQPAQQPYYAPAPeqpVAGNAWQAEEQqSTFAPQSTYQTEQTYQQ 470

                          170       180
                   ....*....|....*....|....*
gi 1820662107  356 PSTKKTYITDPVLAPPSPPMQPKSG 380
Cdd:PRK10263   471 PAAQEPLYQQPQPVEQQPVVEPEPV 495

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.

Pssm-ID: 188714 Cd Length: 56 Bit Score: 39.64 E-value: 2.01e-04

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHR 513
Cdd:cd09328     4 CDSCQDFVEGEVVSALGKTYHPKCFVCSVCRQ 35

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.

Pssm-ID: 188796 [Multi-domain] Cd Length: 52 Bit Score: 39.33 E-value: 2.09e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVVGegtGC-TAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09412     1 CGSCGLPITG---RCiSALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

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.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 39.20 E-value: 2.32e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09345     1 CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

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.

Pssm-ID: 188782 [Multi-domain] Cd Length: 53 Bit Score: 39.16 E-value: 2.44e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIME-RILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNIH 529
Cdd:cd09396     1 CAGCKSEIGHgRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYH 49

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 43.90 E-value: 2.86e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 132 DLESSSP--YKPRTQQGSGFTTSSPVTSPPGSTPVTGHKRMIIP------------NQPPLTATKKSTAKAPMQPAALPA 197
Cdd:PHA03378  547 DIESDEPasTEPVHDQLLPAPGLGPLQIQPLTSPTTSQLASSAPsyaqtpwpvphpSQTPEPPTTQSHIPETSAPRQWPM 626

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 198 PVPVTPVGTLKPQPQPvpasyitastptrpaFNVQVKtaqPSPHFQPPGPPPVQYGLGSNQSYAPQPARPPGPA-----Q 272
Cdd:PHA03378  627 PLRPIPMRPLRMQPIT---------------FNVLVF---PTPHQPPQVEITPYKPTWTQIGHIPYQPSPTGANtmlpiQ 688

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 273 YVPSQPRGPdyGYAPQPARPsePGYGYVPSQgRYQDLYYPAGPGYGGRNGSEPSYVPQNTWKLEPAYPTANTVAQNPPGT 352
Cdd:PHA03378  689 WAPGTMQPP--PRAPTPMRP--PAAPPGRAQ-RPAAATGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGR 763

                         250       260       270
                  ....*....|....*....|....*....|
gi 1820662107 353 YQPPSTK--KTYITDPVLAPPSPPMQPKSG 380
Cdd:PHA03378  764 ARPPAAApgAPTPQPPPQAPPAPQQRPRGA 793

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.

Pssm-ID: 188806 Cd Length: 62 Bit Score: 39.12 E-value: 2.87e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 418 YFGRCSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCYIN 477
Cdd:cd09422     1 YSNTCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLCTECYSN 60

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.

Pssm-ID: 188779 Cd Length: 56 Bit Score: 38.84 E-value: 3.69e-04

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGI 518
Cdd:cd09393     1 CASCGKSIEDECIKFEDKRWHLKCFTCSRCHREISSE 37

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.

Pssm-ID: 188743 Cd Length: 63 Bit Score: 38.94 E-value: 3.85e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 422 CSRCGENVVGE-GTGCT----AMDQVFHVECFTCVTCGNKL----RGQPFYAVEKKAYCEPC 474
Cdd:cd09357     1 CSVCGEPIMPEpGQDETvrivALDRSFHVNCYKCEDCGMLLssedEGQGCYPLDGHLLCKSC 62

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.

Pssm-ID: 188728 Cd Length: 57 Bit Score: 38.91 E-value: 3.88e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHV--ECFTCVTCGNKLRGQPFYAVEKKAYCEP 473
Cdd:cd09342     1 CDACGEPIGPDVQRVAHNGQHWHAteECFCCSNCKKSLLGQPFLPKNGQIFCSP 54

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 43.44 E-value: 4.10e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 179 TATKKSTAKAPMQPAALPAPVPvtpvgtlkPQPQPVPASYITASTPTRPAFNVQVKTAQPSPHFQPPGPPPvqyGLGSNQ 258
Cdd:PRK07764  598 EGPPAPASSGPPEEAARPAAPA--------APAAPAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVP---DASDGG 666

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 259 SYAPQPARPPGPAQYVPSQPRGPDYGYAPQPARPSEPGYGYVPSQGRYQDLY-YPAGPGYGGRNGS-----------EPS 326
Cdd:PRK07764  667 DGWPAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAaQPPQAAQGASAPSpaaddpvplppEPD 746

                         170       180       190
                  ....*....|....*....|....*....|..
gi 1820662107 327 YVPQNTWKLEPAYPTANTVAQNPPGTYQPPST 358
Cdd:PRK07764  747 DPPDPAGAPAQPPPPPAPAPAAAPAAAPPPSP 778

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.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 38.52 E-value: 4.23e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMChrsldGIPFTVDA----GGNIHCIEDF 534
Cdd:cd09337     1 CAYCNGPILDKCVTALDKTWHPEHFFCAQC-----GKPFGDEGfhekDGKPYCREDY 52

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.

Pssm-ID: 188745 Cd Length: 53 Bit Score: 38.40 E-value: 4.44e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVV-GEGTGCtaMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09359     1 CARCGKIVYpTEKVNC--LDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 38.57 E-value: 4.64e-04

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1820662107 440 DQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09343    23 DRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

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.

Pssm-ID: 188816 Cd Length: 56 Bit Score: 38.61 E-value: 4.71e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 482 CSVCAKPIM----ERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDaGGNIHCIE 532
Cdd:cd09432     1 CAACGKPITgiggTKFISFEDRHWHNDCFNCAGCRTSLVGKGFITD-GGRILCPD 54

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).

Pssm-ID: 188784 Cd Length: 61 Bit Score: 38.56 E-value: 4.71e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 542 CSVCKEPIMPAPgqeetiRIVALDRDFHVQCYRCEDCGGLLSEGdnqGCYPLD-GHILCKTC 602
Cdd:cd09400     5 CASCGLPVFLAE------RLLIEGKVYHRTCFKCARCGVQLTPG---SFYETEyGSYCCETC 57

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.

Pssm-ID: 188716 Cd Length: 56 Bit Score: 38.49 E-value: 4.91e-04

                          10        20        30
                  ....*....|....*....|....*....|.
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCH 512
Cdd:cd09330     1 CEACDKFITGKVLEAGGKHYHPTCARCSRCG 31

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.

Pssm-ID: 188783 [Multi-domain] Cd Length: 58 Bit Score: 38.40 E-value: 4.95e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 422 CSRCGENVV--------GEGTGctamdqVFHVECFTCVTCGNKLRGQ-PFYAVEKKAYCEPCY 475
Cdd:cd09397     1 CRKCGLEIEgksisskdGELSG------QWHRECFVCTTCGCPFQFSvPCYVLDDKPYCQQHY 57

The second LIM domain of Testin; The second LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Knockout mice experiments reveal that tumor repressor function of testin. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188800 Cd Length: 56 Bit Score: 38.30 E-value: 5.04e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 421 RCSRCGEnVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCYI 476
Cdd:cd09416     2 RCAGCDE-LIFSNEYTQAENQNWHLKHFCCFDCDNILAGEIYVMVNDKPVCKPCYM 56

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.

Pssm-ID: 188744 [Multi-domain] Cd Length: 53 Bit Score: 38.40 E-value: 5.10e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1820662107 422 CSRCGENV------VGEGTgctamdqVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEP 473
Cdd:cd09358     1 CAVCGKTVypmerlVADGK-------LFHKSCFRCSHCNKTLRLGNYASLEGKLYCKP 51

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.

Pssm-ID: 188754 Cd Length: 52 Bit Score: 38.17 E-value: 5.62e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTvdAGGNIHCIEDF 534
Cdd:cd09368     1 CGGCQEHILDRfILKVLDRTWHAKCLKCNDCGAQLTDKCFA--RNGHVYCKDDF 52

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.

Pssm-ID: 188776 Cd Length: 55 Bit Score: 38.30 E-value: 5.64e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAK--PIMERILRATGKAYHPHCFTCVMC-HRSLDGIPFTVdAGGNIHCIEDF 534
Cdd:cd09390     1 CAACSKtiPAFEMVMRARTNVYHLECFACQRCnHRFCVGDRFYL-CENKILCEYDY 55

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.

Pssm-ID: 188846 [Multi-domain] Cd Length: 74 Bit Score: 38.71 E-value: 6.10e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 540 PRCSVCKEPIMPapGQeetiRIVALDRDFHVQCYRCEDCGGLLSegdnQGCYPLDGHILCK 600
Cdd:cd09462    20 PVCASCGQSIYD--GQ----YLQALNSDWHADCFRCCECGASLS----HWYYEKDGRLFCK 70

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.

Pssm-ID: 188761 Cd Length: 56 Bit Score: 38.11 E-value: 6.15e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLR-GQPFYAVEKKAY-CEPCY 475
Cdd:cd09375     1 CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLStGEELYILDENKFiCKEDY 56

The second LIM domain of Arrowhead (AWH); The second 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.

Pssm-ID: 188765 Cd Length: 55 Bit Score: 38.17 E-value: 6.22e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 542 CSVCKEPIMPApgqeETIRiVALDRDFHVQCYRCEDCGGLLSEGDNQGCypLDGHILCKT 601
Cdd:cd09379     1 CAKCSRNISAS----DWVR-RARDHVYHLACFACDACKRQLSTGEEFAL--IEDRVLCKA 53

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.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 38.07 E-value: 6.26e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 482 CSVCAKPI--MERILRAtGKAYHPHCFTCVMCHRSLDGIPFTvDAGGNIHC 530
Cdd:cd09482     1 CPRCGKSVyaAEKVMGG-GKPWHKTCFRCAICGKSLESTTVT-DKDGELYC 49

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.

Pssm-ID: 188845 Cd Length: 54 Bit Score: 37.92 E-value: 7.46e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09461     1 CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGGRPFCK 51

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.

Pssm-ID: 188749 [Multi-domain] Cd Length: 54 Bit Score: 37.80 E-value: 7.62e-04

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPF 520
Cdd:cd09363     1 CHGCDFPIEagDRFLEALGHTWHDTCFVCAVCHVNLEGQTF 41

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 42.67 E-value: 7.72e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 134 ESSSPYKPRTQQGSGFTTSSPVTSPPGSTPVTGHKRMIIPNQPPLTATKKSTAKAPMQPAALPAPVPVTPvGTLKPQPQP 213
Cdd:PRK07764  623 APAAPAPAGAAAAPAEASAAPAPGVAAPEHHPKHVAVPDASDGGDGWPAKAGGAAPAAPPPAPAPAAPAA-PAGAAPAQP 701

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 214 VPASyitasTPTRPAFNVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAPQPARPPGPAQYVPSQPRGP----DYGYAPQP 289
Cdd:PRK07764  702 APAP-----AATPPAGQADDPAAQPPQAAQGASAPSPAADDPVPLPPEPDDPPDPAGAPAQPPPPPAPapaaAPAAAPPP 776


                  ....*.
gi 1820662107 290 ARPSEP 295
Cdd:PRK07764  777 SPPSEE 782

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.

Pssm-ID: 188852 Cd Length: 52 Bit Score: 37.64 E-value: 7.77e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTvdAGGNIHCIEDF 534
Cdd:cd09468     1 CAGCNQHILDKfILKVLDRHWHSSCLKCADCQMQLAERCFS--RAGNVYCKEDF 52

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.

Pssm-ID: 188858 Cd Length: 59 Bit Score: 38.14 E-value: 7.98e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 421 RCSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKL-RGQPFYAVEKKAYC 471
Cdd:cd09474     4 RCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLtTGDHFGMKDNLVYC 55

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.

Pssm-ID: 188736 Cd Length: 54 Bit Score: 37.77 E-value: 8.10e-04

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 542 CSVCKEPIMpapGQEETIriVALDRDFHVQCYRCEDCGGLLSegdNQGCYPLDGHILCKTC 602
Cdd:cd09350     1 CGRCGENVV---GEGTGC--TAMDQVFHVDCFTCMTCNGKLR---GQPFYAVEKKAYCEPC 53

The first LIM domain of Cysteine Rich Protein 1 (CRP1); The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188863 Cd Length: 56 Bit Score: 37.69 E-value: 8.39e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 480 EQCSVCAKPI-MERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDaGGNIHC 530
Cdd:cd09479     1 KKCGVCQKTVyFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVH-GEEIYC 51

flagellar motor protein MotB; Reviewed

Pssm-ID: 183756 [Multi-domain] Cd Length: 421 Bit Score: 42.01 E-value: 8.61e-04

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 115 RRSSLDAEIDSLTSILADLEssspyKPRTQQGSGFTTSSPVTSPPGSTPVTghkrmiipnqpPLTATKKSTAKAPmQPAA 194
Cdd:PRK12799  266 KQSQHDIEHENLDNRALDIE-----KATGLKQIDTHGTVPVAAVTPSSAVT-----------QSSAITPSSAAIP-SPAV 328

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 195 LPAPVPVTPVGTLKPQPQPVPASYITASTPTRPAFNVQVKTAQPSPHFQPPGPPPVQYGL-GSNQSYAPQP--ARPPGPA 271
Cdd:PRK12799  329 IPSSVTTQSATTTQASAVALSSAGVLPSDVTLPGTVALPAAEPVNMQPQPMSTTETQQSStGNITSTANGPttSLPAAPA 408

                         170
                  ....*....|.
gi 1820662107 272 QYVPSQPRGPD 282
Cdd:PRK12799  409 SNIPVSPTSRD 419

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.

Pssm-ID: 188761 Cd Length: 56 Bit Score: 37.73 E-value: 9.78e-04

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLD-GIPFTVDAGGNIHCIEDF 534
Cdd:cd09375     1 CAGCDQGISpnDLVRRARDKVFHLNCFTCMVCRKQLStGEELYILDENKFICKEDY 56

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.

Pssm-ID: 188758 [Multi-domain] Cd Length: 53 Bit Score: 37.40 E-value: 1.04e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGEnVVGEGTgCTAMDQVFHVECFTCVTCGNKLRGQPFyAVEK--KAYCEPCY 475
Cdd:cd09372     1 CAKCQG-VITEHI-IRALGKGYHPPCFTCVTCGRRIGDESF-AVDEqnEVYCLDDY 53

Topoisomerase II-associated protein PAT1; Members of this family are necessary for accurate chromosome transmission during cell division.

Pssm-ID: 401645 [Multi-domain] Cd Length: 846 Bit Score: 41.95 E-value: 1.10e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 191 QPAALPAPVPVTPVGTLKPQPQPVPASYITASTPTRPAFN----------VQVKTA-------QPSPHFQPPGPPPVQYG 253
Cdd:pfam09770 106 QPAARAAQSSAQPPASSLPQYQYASQQSQQPSKPVRTGYEkykepepipdLQVDASlwgvapkKAAAPAPAPQPAAQPAS 185

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 254 LGSN----------------QSYAPQPARPPGPAQyvpsQPRGPDYGYAPQPARPSEPGYGYVPSQGRYQDLYYPAGPGY 317
Cdd:pfam09770 186 LPAPsrkmmsleeveaamraQAKKPAQQPAPAPAQ----PPAAPPAQQAQQQQQFPPQIQQQQQPQQQPQQPQQHPGQGH 261

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 318 ----------GGRNGSEPSYVPQNTWKLEPAYPTANT---VAQNPPgtyQPPSTKKTYITDPVLAPPSPPMQPKSGYPAS 384
Cdd:pfam09770 262 pvtilqrpqsPQPDPAQPSIQPQAQQFHQQPPPVPVQptqILQNPN---RLSAARVGYPQNPQPGVQPAPAHQAHRQQGS 338

                         250
                  ....*....|....*....
gi 1820662107 385 gSGSNAPLFRPEDELEHLT 403
Cdd:pfam09770 339 -FGRQAPIITHPQQLAQLS 356

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP); The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188865 Cd Length: 54 Bit Score: 37.43 E-value: 1.11e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 421 RCSRCGENVV-GEGTGCTAmdQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09481     1 KCGACEKTVYhAEEIQCNG--RSFHKTCFICMACRKALDSTTVAAHESEIYCKTCY 54

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.

Pssm-ID: 188720 [Multi-domain] Cd Length: 54 Bit Score: 37.33 E-value: 1.15e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPF 520
Cdd:cd09334     3 CGACRRPIEGRVVTALGKHWHVEHFVCAKCEKPFLGHRH 41

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.

Pssm-ID: 188731 [Multi-domain] Cd Length: 54 Bit Score: 37.27 E-value: 1.16e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHC 530
Cdd:cd09345     1 CKACGKAIMpgSKKMEYKGKFWHEKCFTCSECKKPIGTKSF-IPKDDKIYC 50

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.

Pssm-ID: 188764 Cd Length: 55 Bit Score: 37.43 E-value: 1.18e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKL-RGQPFYAVEKKAYCEPCY 475
Cdd:cd09378     1 CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLqKGDEFVLKEGQLLCKSDY 55

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.

Pssm-ID: 188811 Cd Length: 58 Bit Score: 37.52 E-value: 1.23e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 421 RCSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09427     3 KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYCVPCY 57

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.

Pssm-ID: 188778 [Multi-domain] Cd Length: 53 Bit Score: 36.95 E-value: 1.30e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 422 CSRCGENVvgEGTGCTAMDQVFHVECFTCVTCGNKLRGQ-PFYAVEKKAYCE 472
Cdd:cd09392     1 CFKCGGAL--RGSYITALGRKYHVEHFTCSVCPTVFGPNdSYYEHEGKIYCH 50

The second LIM domain of Lhx6; The second LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188768 Cd Length: 55 Bit Score: 37.37 E-value: 1.34e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLR-GQPFYAVEKKAYCEPCY 475
Cdd:cd09382     1 CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLStGEEFGLVEEKVLCRIHY 55

Atrophin-1 family; Atrophin-1 is the protein product of the dentatorubral-pallidoluysian atrophy (DRPLA) gene. DRPLA OMIM:125370 is a progressive neurodegenerative disorder. It is caused by the expansion of a CAG repeat in the DRPLA gene on chromosome 12p. This results in an extended polyglutamine region in atrophin-1, that is thought to confer toxicity to the protein, possibly through altering its interactions with other proteins. The expansion of a CAG repeat is also the underlying defect in six other neurodegenerative disorders, including Huntington's disease. One interaction of expanded polyglutamine repeats that is thought to be pathogenic is that with the short glutamine repeat in the transcriptional coactivator CREB binding protein, CBP. This interaction draws CBP away from its usual nuclear location to the expanded polyglutamine repeat protein aggregates that are characteriztic of the polyglutamine neurodegenerative disorders. This interferes with CBP-mediated transcription and causes cytotoxicity.

Pssm-ID: 460830 [Multi-domain] Cd Length: 991 Bit Score: 42.06 E-value: 1.34e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 134 ESSSPYKPRTQQGSGFTTSSPVTSPPGSTPvtghkrmiIPNQPpltatkksTAKAPMQPAALPAPVPVTPVGTLKPQPQP 213
Cdd:pfam03154 333 QLQSQQPPREQPLPPAPLSMPHIKPPPTTP--------IPQLP--------NPQSHKHPPHLSGPSPFQMNSNLPPPPAL 396

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 214 VPASYITASTPtrpafnvqvKTAQPSPhfqppgpppVQYgLGSNQSYAPQPARPPGPAQyVPSQPrgpdygyAPQPARPS 293
Cdd:pfam03154 397 KPLSSLSTHHP---------PSAHPPP---------LQL-MPQSQQLPPPPAQPPVLTQ-SQSLP-------PPAASHPP 449

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 294 EPGYGYVPSQGRY-QDLYYPAGPGYGGRNGSEPSYVPQNTWKLEPAYPTANTVAQNPPGTYQ---PPSTKKTYITDPVLA 369
Cdd:pfam03154 450 TSGLHQVPSQSPFpQHPFVPGGPPPITPPSGPPTSTSSAMPGIQPPSSASVSSSGPVPAAVScplPPVQIKEEALDEAEE 529

                         250
                  ....*....|...
gi 1820662107 370 PPSPPMQPKSGYP 382
Cdd:pfam03154 530 PESPPPPPRSPSP 542

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.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 37.16 E-value: 1.35e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 1820662107 481 QCSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPF 520
Cdd:cd09421     4 QCEECSKIIGidSKDLSYKDKHWHEACFLCSKCKISLVDKPF 45

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.

Pssm-ID: 188859 Cd Length: 59 Bit Score: 37.37 E-value: 1.35e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 421 RCSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLR-GQPFYAVEKKAYC 471
Cdd:cd09475     4 RCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTtGDHFGMKDNLVYC 55

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.

Pssm-ID: 188845 Cd Length: 54 Bit Score: 37.15 E-value: 1.37e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAG 525
Cdd:cd09461     1 CVSCGFPIEagDRWVEALNNNYHSQCFNCTRCNVNLEGQSFYAKGG 46

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.

Pssm-ID: 188837 [Multi-domain] Cd Length: 52 Bit Score: 36.92 E-value: 1.39e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHC 530
Cdd:cd09453     1 CATCNQVIRGPFLVALGKSWHPEEFNCAHCKSSMAYIGF-VEEKGALYC 48

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.

Pssm-ID: 188772 [Multi-domain] Cd Length: 55 Bit Score: 37.02 E-value: 1.39e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1820662107 563 ALDRDFHVQCYRCEDCGGLLSEgDNQGCYPLDGHILCKT 601
Cdd:cd09386    16 ALDRYWHNGCLKCSCCQAQLGE-IGSSCYTKGGMILCKN 53

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.

Pssm-ID: 188724 [Multi-domain] Cd Length: 53 Bit Score: 36.93 E-value: 1.43e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09338     1 CGGCNKPILENYI--SALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 52

DNA polymerase III subunits gamma and tau; Validated

Pssm-ID: 236090 [Multi-domain] Cd Length: 824 Bit Score: 41.51 E-value: 1.52e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 151 TSSPVTSPPGSTPVTGHKRMIIPNQP-PLTATKKSTAKAPMQPAALPAPVPVTPVGTLKP---QPQPVPASYITASTPTR 226
Cdd:PRK07764  590 PAPGAAGGEGPPAPASSGPPEEAARPaAPAAPAAPAAPAPAGAAAAPAEASAAPAPGVAApehHPKHVAVPDASDGGDGW 669

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 227 PAFNVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAPQPARPPGPAQYVPSQPRGPDYGYAPQPAR-------PSEPGYGY 299
Cdd:PRK07764  670 PAKAGGAAPAAPPPAPAPAAPAAPAGAAPAQPAPAPAATPPAGQADDPAAQPPQAAQGASAPSPAaddpvplPPEPDDPP 749

                         170       180       190
                  ....*....|....*....|....*....|.
gi 1820662107 300 VPSQGrYQDLYYPAGPGYGGRNGSEPSYVPQ 330
Cdd:PRK07764  750 DPAGA-PAQPPPPPAPAPAAAPAAAPPPSPP 779

The first LIM domain of Isl, a member of LHX protein family; The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188752 [Multi-domain] Cd Length: 55 Bit Score: 36.94 E-value: 1.55e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 542 CSVCKEPImpapgQEETIRIVALDRDFHVQCYRCEDCGGLLSEgdNQGCYPLDGHILCKTC 602
Cdd:cd09366     1 CVGCGGKI-----HDQYILRVAPDLEWHAACLKCAECGQYLDE--TCTCFVRDGKTYCKRD 54

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.

Pssm-ID: 188777 Cd Length: 57 Bit Score: 36.90 E-value: 1.63e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGN 455
Cdd:cd09391     1 CAKCGKPITGQFV--RALGDVYHLDCFTCHDCGK 32

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.

Pssm-ID: 188792 [Multi-domain] Cd Length: 52 Bit Score: 36.72 E-value: 1.65e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRsLDGIPFTVDAGGNIHCIEDF 534
Cdd:cd09408     1 CAYCAGPILQNVLTAMDQTWHPEHFFCSHCGE-LFGDEGFLERDGKPYCRRDF 52

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.

Pssm-ID: 188809 Cd Length: 54 Bit Score: 37.03 E-value: 1.67e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1820662107 441 QVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09425    20 QQWHEKCFCCCECKQPIGTKSFIPKDDDVYCVPCY 54

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.

Pssm-ID: 188805 Cd Length: 59 Bit Score: 37.16 E-value: 1.69e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09421     5 CEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 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.

Pssm-ID: 188723 [Multi-domain] Cd Length: 52 Bit Score: 36.60 E-value: 1.77e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1820662107 437 TAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYC 471
Cdd:cd09337    14 TALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYC 48

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.

Pssm-ID: 188746 [Multi-domain] Cd Length: 52 Bit Score: 36.58 E-value: 1.88e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSL 515
Cdd:cd09360     1 CDKCGNGIVGVVVKARDKNRHPECFVCADCGLNL 34

The second LIM domain of LIMK1 (LIM domain Kinase 1); The second 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.

Pssm-ID: 188848 Cd Length: 55 Bit Score: 36.78 E-value: 1.97e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGENVVgEGTGCTAMDQVFHVECFTCVTCGNKL-RGQPFYAVEK-KAYCEPCY 475
Cdd:cd09464     1 CHGCSETIT-TGLVMVAGEQKYHPECFSCLRCGAFIgDGDTYALVEHsKLYCGHCY 55

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.

Pssm-ID: 188795 [Multi-domain] Cd Length: 52 Bit Score: 36.47 E-value: 2.01e-03

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLD 516
Cdd:cd09411     1 CSGCQKPITGRCITAMGKKFHPEHFVCAFCLKQLN 35

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.

Pssm-ID: 188735 [Multi-domain] Cd Length: 87 Bit Score: 37.53 E-value: 2.07e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*
gi 1820662107 478 TLEQCSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPF 520
Cdd:cd09349    30 TNELCGICGQPLSrtQPAVRALGHLFHVTCFTCHQCEQQLQGQQF 74

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.

Pssm-ID: 188715 [Multi-domain] Cd Length: 52 Bit Score: 36.53 E-value: 2.23e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1820662107 542 CSVCKEPImpAPGQEetirIVALDRDFHVQCYRCEDCGGLLSE 584
Cdd:cd09329     1 CAGCGQEI--KNGQA----LLALDKQWHVWCFKCKECGKVLTG 37

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.

Pssm-ID: 188744 [Multi-domain] Cd Length: 53 Bit Score: 36.48 E-value: 2.37e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1820662107 542 CSVCKEPIMPApgqeEtiRIVALDRDFHVQCYRCEDCGGLLSEGDNQGcypLDGHILCK 600
Cdd:cd09358     1 CAVCGKTVYPM----E--RLVADGKLFHKSCFRCSHCNKTLRLGNYAS---LEGKLYCK 50

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.

Pssm-ID: 188857 Cd Length: 56 Bit Score: 36.54 E-value: 2.47e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAK--PIMERILRATGKAYHPHCFTCVMCHRSL-DGIPFTVDAGGNIHCIEDF 534
Cdd:cd09473     1 CTACQQgiPPTQVVRKAQDFVYHLHCFACIICSRQLaTGDEFYLMEDGRLVCKEDY 56

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.

Pssm-ID: 188841 [Multi-domain] Cd Length: 52 Bit Score: 36.16 E-value: 2.58e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDaGGNIHCIEDF 534
Cdd:cd09457     1 CGRCQRKILGEVINALKQTWHVSCFVCVACHNPIRNNVFHLE-DGEPYCETDY 52

The LIM domain of Mlp84B and Mlp60A; The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

Pssm-ID: 188788 Cd Length: 54 Bit Score: 36.31 E-value: 2.73e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1820662107 481 QCSVCAKPIM---ERIlrATGKAYHPHCFTCVMCHRSLD 516
Cdd:cd09404     1 KCPKCGKSVYaaeERL--AGGYKWHKMCFKCGMCNKLLD 37

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.

Pssm-ID: 188796 [Multi-domain] Cd Length: 52 Bit Score: 36.25 E-value: 2.76e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGgnihciedfhkkfAPRCSVC 545
Cdd:cd09412     1 CGSCGLPITGRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSG-------------KPYCSTC 51

DNA polymerase III subunits gamma and tau; Provisional

Pssm-ID: 237865 [Multi-domain] Cd Length: 618 Bit Score: 40.85 E-value: 2.79e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 183 KSTAKAPMQPAALPAPVPVTPVGTLkpqPQPVPASyITASTPTRPAFNVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAP 262
Cdd:PRK14951  378 KKTPARPEAAAPAAAPVAQAAAAPA---PAAAPAA-AASAPAAPPAAAPPAPVAAPAAAAPAAAPAAAPAAVALAPAPPA 453

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1820662107 263 QPARP---------PGPAqyVPSQPRGPDYGYAPQPARPSEPG 296
Cdd:PRK14951  454 QAAPEtvaipvrvaPEPA--VASAAPAPAAAPAAARLTPTEEG 494

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.

Pssm-ID: 188763 Cd Length: 59 Bit Score: 36.48 E-value: 2.80e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSL 515
Cdd:cd09377     5 CARCHLGISasELVMRARDLVFHLNCFTCATCNKPL 40

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.

Pssm-ID: 188840 [Multi-domain] Cd Length: 52 Bit Score: 36.13 E-value: 2.80e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDAGGNiHCIEDF 534
Cdd:cd09456     1 CAKCKKKITGEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAP-YCERDY 52

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).

Pssm-ID: 188784 Cd Length: 61 Bit Score: 36.25 E-value: 2.86e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1820662107 442 VFHVECFTCVTCGNKLRGQPFYAVEKKAY-CEPC 474
Cdd:cd09400    24 VYHRTCFKCARCGVQLTPGSFYETEYGSYcCETC 57

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.

Pssm-ID: 188822 Cd Length: 62 Bit Score: 36.22 E-value: 3.09e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 422 CSRCGENVV-GEGTGCT----AMDQVFHVECFTCVTCGNKLRGQP---FYAVEKKAYCEPCY 475
Cdd:cd09438     1 CAACGQPILpAEGSEETirvvSMDKDYHVECYHCEDCGLQLNDEEghrCYPLDGHLLCHSCH 62

DNA polymerase III subunit gamma/tau;

Pssm-ID: 237057 [Multi-domain] Cd Length: 700 Bit Score: 40.63 E-value: 3.31e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 153 SPVTSPPGSTPVTGHKRMIIPNQPPLTATKKSTAKAPMQPAALPAPVPVtPVGTLKP---QPQPVPASYITASTPTRPAF 229
Cdd:PRK12323  409 APAAAAAARAVAAAPARRSPAPEALAAARQASARGPGGAPAPAPAPAAA-PAAAARPaaaGPRPVAAAAAAAPARAAPAA 487

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 230 -------------NVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAPQPA-----RPPGPAQYVPSQPRGPDYGYAPQPAR 291
Cdd:PRK12323  488 apapadddpppweELPPEFASPAPAQPDAAPAGWVAESIPDPATADPDDafetlAPAPAAAPAPRAAAATEPVVAPRPPR 567


                  ....*
gi 1820662107 292 PSEPG 296
Cdd:PRK12323  568 ASASG 572

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.

Pssm-ID: 188750 [Multi-domain] Cd Length: 53 Bit Score: 35.93 E-value: 3.57e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1820662107 542 CSVCKEPIMPAPgqeetiRIVALDRDFHVQCYRCEDCGGLLSegdNQgCYPLDGHILCK 600
Cdd:cd09364     1 CAGCRGKILDSQ------YVQALNQDWHCDCFRCSVCSDSLS---NW-YFEKDGKLYCR 49

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.

Pssm-ID: 188813 Cd Length: 53 Bit Score: 35.94 E-value: 3.74e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFT 521
Cdd:cd09429     1 CVKCNKPITSGGVTYQDQPWHSECFVCSSCSKKLAGQRFT 40

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.

Pssm-ID: 188780 Cd Length: 55 Bit Score: 35.80 E-value: 3.86e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGENVVgEGTGCTAMDQVFHVECFTCVTCGNKL 457
Cdd:cd09394     1 CVGCKESIT-EGHAYELGGDRWHIHCFKCYKCDKKL 35

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.

Pssm-ID: 188843 [Multi-domain] Cd Length: 55 Bit Score: 35.71 E-value: 4.02e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPFtvdaggnihciedFHKKFAPRC 542
Cdd:cd09459     1 CHGCEFPIEagDRFLEALGHTWHDTCFVCSVCCESLEGQTF-------------FSKKDKPLC 50

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.

Pssm-ID: 188807 Cd Length: 59 Bit Score: 36.05 E-value: 4.07e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09423     5 CDECKELIGHDSRELYYEDRHYHEHCFRCFRCDRSLADEPFTCQDEELLCNDCY 58

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.

Pssm-ID: 188828 [Multi-domain] Cd Length: 55 Bit Score: 35.85 E-value: 4.20e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPI--MERILrATGKAYHPHCFTCVMCHRSL 515
Cdd:cd09444     1 CAACGQHVhlVQRHL-VDGKLYHRNCFRCKECSSTL 35

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.

Pssm-ID: 188869 [Multi-domain] Cd Length: 53 Bit Score: 35.63 E-value: 4.40e-03

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1820662107 438 AMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09485    16 ANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

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.

Pssm-ID: 188807 Cd Length: 59 Bit Score: 35.67 E-value: 4.72e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 1820662107 475 YINTLEQCsvcaKPIME---RILRATGKAYHPHCFTCVMCHRSLDGIPFT 521
Cdd:cd09423     1 FANTCDEC----KELIGhdsRELYYEDRHYHEHCFRCFRCDRSLADEPFT 46

Uncharacterized conserved protein, contains PIN-related Mut7-C RNAse domain [General function prediction only];

Pssm-ID: 441262 Cd Length: 155 Bit Score: 37.92 E-value: 4.75e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1820662107 541 RCSVCKEPIMPAPGQEETIRIVALDRDFHVQCYRCEDCG 579
Cdd:COG1656    92 RCLRCNGPLEPVDKEEVADRVPPYVRERYDEFWRCPKCG 130

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.

Pssm-ID: 188830 Cd Length: 53 Bit Score: 35.66 E-value: 4.82e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|..
gi 1820662107 422 CSRCGENVV-GEGTGCtaMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCE 472
Cdd:cd09446     1 CARCGYGVYpAEKINC--IDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQ 50

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.

Pssm-ID: 188852 Cd Length: 52 Bit Score: 35.33 E-value: 5.16e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1820662107 542 CSVCKEPIMpapgqeETIRIVALDRDFHVQCYRCEDCGGLLSEgdnqGCYPLDGHILCK 600
Cdd:cd09468     1 CAGCNQHIL------DKFILKVLDRHWHSSCLKCADCQMQLAE----RCFSRAGNVYCK 49

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.

Pssm-ID: 188808 Cd Length: 58 Bit Score: 35.51 E-value: 5.51e-03

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1820662107 442 VFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09424    21 VWHKDCFTCSNCKQPIGTKSFFPKGEDFYCVPCH 54

multifunctional oxoglutarate decarboxylase/oxoglutarate dehydrogenase thiamine pyrophosphate-binding subunit/dihydrolipoyllysine-residue succinyltransferase subunit;

Pssm-ID: 237030 [Multi-domain] Cd Length: 1228 Bit Score: 39.87 E-value: 5.65e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  149 FTTSSPVTSPPGSTPVTGHKrmiiPNQPPLTATKKSTAKAPMQPAALPAPVPVTPvgtlkPQPQPVPASYITASTPTRPA 228
Cdd:PRK12270    33 FADYGPGSTAAPTAAAAAAA----AAASAPAAAPAAKAPAAPAPAPPAAAAPAAP-----PKPAAAAAAAAAPAAPPAAA 103

                           90
                   ....*....|....*
gi 1820662107  229 FNVQVKTAQPSPHFQ 243
Cdd:PRK12270   104 AAAAPAAAAVEDEVT 118

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.

Pssm-ID: 188733 Cd Length: 56 Bit Score: 35.40 E-value: 5.71e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1820662107 422 CSRCGENVVGEGtGCTAM---DQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPC 474
Cdd:cd09347     1 CAACTKPITGLG-GAKFIsfeERQWHSDCFNCGKCSVSLVGQGFLTQRDEILCPEC 55

large tegument protein UL36; Provisional

Pssm-ID: 223021 [Multi-domain] Cd Length: 3151 Bit Score: 39.92 E-value: 5.75e-03

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107  262 PQPA-RPPGPAqyVPSQPRGPDYgyAPQPARPSEPGygyvpsqgryqdlyypaGPGYGGRNGSEPSYVPQNTWKLEPAyP 340
Cdd:PHA03247  2571 PRPApRPSEPA--VTSRARRPDA--PPQSARPRAPV-----------------DDRGDPRGPAPPSPLPPDTHAPDPP-P 2628

                           90       100       110       120       130       140       150
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1820662107  341 TANTVAQNPPGTYQPPSTKKTYITDPVLAPPSPPMQPKSGYPASGSGSNAPLFRPEDELEHLTKKMLYDMENPP 414
Cdd:PHA03247  2629 PSPSPAANEPDPHPPPTVPPPERPRDDPAPGRVSRPRRARRLGRAAQASSPPQRPRRRAARPTVGSLTSLADPP 2702

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.

Pssm-ID: 188748 [Multi-domain] Cd Length: 52 Bit Score: 35.15 E-value: 5.86e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPFTVDaGGNIHCIEDF 534
Cdd:cd09362     1 CARCHKKILGEVMHALKQTWHVSCFVCAACKQPIGNSLFHME-DGEPYCEKDY 52

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.

Pssm-ID: 188747 [Multi-domain] Cd Length: 52 Bit Score: 35.41 E-value: 5.87e-03

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1820662107 422 CSRCgeNVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09361     1 CAHC--NQVIRGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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.

Pssm-ID: 188794 [Multi-domain] Cd Length: 53 Bit Score: 35.18 E-value: 6.40e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRS--------LDGIPF 520
Cdd:cd09410     1 CSGCGRPVKENYLSAANGVWHPECFVCSDCLKPftdgsffeLDGRPL 47

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.

Pssm-ID: 188729 Cd Length: 59 Bit Score: 35.11 E-value: 6.96e-03

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 1820662107 481 QCSVCAKPIM--ERILRATGKAYHPHCFTCVMCHRSLDGIPFT 521
Cdd:cd09343     4 TCEECKKKIGcdSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFA 46

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.

Pssm-ID: 188725 [Multi-domain] Cd Length: 52 Bit Score: 35.01 E-value: 6.99e-03

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSLDGIPF 520
Cdd:cd09339     1 CAGCGKPITGRCITAMGRKFHPEHFVCAFCLKQLSKGTF 39

EBNA-3B; Provisional

Pssm-ID: 223065 [Multi-domain] Cd Length: 991 Bit Score: 39.67 E-value: 7.15e-03

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 141 PRTQQGSGFTTSSPVTSPPGSTPVTGHKRMIIPNQPPLTATKKSTAKAPMQPAALPapvpvtPVGTLKPQPQPVPASYiT 220
Cdd:PHA03378  655 PQVEITPYKPTWTQIGHIPYQPSPTGANTMLPIQWAPGTMQPPPRAPTPMRPPAAP------PGRAQRPAAATGRARP-P 727

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 221 ASTPTRPAFNVQVKTAQPSPHFQPPGPPPVQYGLGSNQSYAPQPARP-PGPAQYVPSQPRG-PDYGYAPQPARPSEPGYG 298
Cdd:PHA03378  728 AAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGRARPPAAAPGAPtPQPPPQAPPAPQQrPRGAPTPQPPPQAGPTSM 807

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 299 YV-----PSQGRYQDLYYPAGPGYGGRNGSEPSYVPQNTWKLEPAYPTANTVAQNPPGTYQPPstkktYITDPVLAPPSP 373
Cdd:PHA03378  808 QLmpraaPGQQGPTKQILRQLLTGGVKRGRPSLKKPAALERQAAAGPTPSPGSGTSDKIVQAP-----VFYPPVLQPIQV 882

                         250
                  ....*....|...
gi 1820662107 374 PMQPKSGYPASGS 386
Cdd:PHA03378  883 MRQLGSVRAAAAS 895

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.

Pssm-ID: 188866 [Multi-domain] Cd Length: 54 Bit Score: 34.99 E-value: 7.43e-03

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1820662107 422 CSRCG------ENVVGEGtgctamdQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09482     1 CPRCGksvyaaEKVMGGG-------KPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCY 53

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.

Pssm-ID: 188744 [Multi-domain] Cd Length: 53 Bit Score: 34.94 E-value: 7.74e-03

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1820662107 482 CSVCAKPI--MERILrATGKAYHPHCFTCVMCHRSL 515
Cdd:cd09358     1 CAVCGKTVypMERLV-ADGKLFHKSCFRCSHCNKTL 35

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.

Pssm-ID: 188851 [Multi-domain] Cd Length: 55 Bit Score: 34.91 E-value: 7.80e-03

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gi 1820662107 479 LEQCSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTvdAGGNIHCIEDF 534
Cdd:cd09467     1 IPLCAGCNQHIVDRfILKVLDRHWHSKCLKCSDCQTQLAEKCFS--RGDSVYCKDDF 55

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.

Pssm-ID: 188759 [Multi-domain] Cd Length: 54 Bit Score: 35.04 E-value: 7.81e-03

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gi 1820662107 542 CSVCKEPImpapgQEETIRIVAlDRDFHVQCYRCEDCGGLLseGDNQGCYPLDGHILCKT 601
Cdd:cd09373     1 CTGCGEPI-----TDRFLLKVS-GRSWHVSCLRCCVCQTPL--ERQPSCFTRDRQIYCKA 52

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.

Pssm-ID: 188734 Cd Length: 64 Bit Score: 35.12 E-value: 8.41e-03

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gi 1820662107 480 EQCSVCAKPIM-----ERILRATGKAYHPHCFTCVMCHRSLDGIPFtVDAGGNIHCIEDFHK 536
Cdd:cd09348     3 KKCSGCQNPITgfgkgTNVVNYEGSSWHDYCFNCKKCSLNLANKRF-VFHNGQIYCSDCAKK 63

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.

Pssm-ID: 188795 [Multi-domain] Cd Length: 52 Bit Score: 34.93 E-value: 8.65e-03

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gi 1820662107 422 CSRCGENVVGEGTgcTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09411     1 CSGCQKPITGRCI--TAMGKKFHPEHFVCAFCLKQLNKGTFKEQNDKPYCHNCF 52

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.

Pssm-ID: 188855 Cd Length: 55 Bit Score: 34.90 E-value: 8.91e-03

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gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNK-LRGQPFYAVEKKAYC 471
Cdd:cd09471     1 CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQlLPGDEFCLREHELLC 51

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.

Pssm-ID: 130689 [Multi-domain] Cd Length: 562 Bit Score: 39.02 E-value: 8.96e-03

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gi 1820662107 209 PQPQPVPASYitastpTRPAFNvqvktaQPSPHFQPPGPPPVqYGLGSNQSYAPQPARPPGPAQYVP-SQPRGPDYGYAP 287
Cdd:TIGR01628 386 PMGSPMGGAM------GQPPYY------GQGPQQQFNGQPLG-WPRMSMMPTPMGPGGPLRPNGLAPmNAVRAPSRNAQN 452

                          90       100       110
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gi 1820662107 288 QPARPSEPGYGYVP-SQGRYQDLYYPAGPGYGGRNGSEP 325
Cdd:TIGR01628 453 AAQKPPMQPVMYPPnYQSLPLSQDLPQPQSTASQGGQNK 491

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.

Pssm-ID: 188757 [Multi-domain] Cd Length: 53 Bit Score: 34.66 E-value: 9.28e-03

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gi 1820662107 482 CSVCAKPIMER-ILRATGKAYHPHCFTCVMCHRSLDGIPFTVDagGNIHCIEDF 534
Cdd:cd09371     1 CAGCQRPISDRyLLRVNERSWHEECLQCSVCQQPLTTSCYFRD--RKLYCKQDY 52

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.

Pssm-ID: 188776 Cd Length: 55 Bit Score: 34.83 E-value: 9.36e-03

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gi 1820662107 422 CSRCGENVVGEGTGCTAMDQVFHVECFTCVTCGNKL-RGQPFYAVEKKAYCEPCY 475
Cdd:cd09390     1 CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFcVGDRFYLCENKILCEYDY 55

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.

Pssm-ID: 188763 Cd Length: 59 Bit Score: 34.94 E-value: 9.68e-03

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                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1820662107 541 RCSVCKEPIMPApgqEETIRivALDRDFHVQCYRCEDCGGLLSEGDNQGCYplDGHILCKT 601
Cdd:cd09377     4 RCARCHLGISAS---ELVMR--ARDLVFHLNCFTCATCNKPLTKGDHFGMR--DGLVYCRL 57

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.

Pssm-ID: 188835 Cd Length: 53 Bit Score: 34.91 E-value: 9.73e-03

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gi 1820662107 482 CSVCAKPIMERILRATGKAYHPHCFTCVMCHRSL 515
Cdd:cd09451     1 CTRCGNGIVGTIVKARDKLYHPECFMCDDCGLNL 34

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.

Pssm-ID: 188838 [Multi-domain] Cd Length: 52 Bit Score: 34.57 E-value: 9.73e-03

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gi 1820662107 422 CSRCgeNVVGEGTGCTAMDQVFHVECFTCVTCGNKLRGQPFYAVEKKAYCEPCY 475
Cdd:cd09454     1 CGHC--NNIIRGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52