calponin homology (CH) domain found in LIM and calponin homology domains-containing protein 1; LIM and calponin homology domains-containing protein 1 (LIMCH1) acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. LIMCH1 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   23 AFSEAQKWIEQVTGRSFGDKDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDP 102
Cdd:cd21278     1 AFTEAQKWIEQVTGRSFGDKDFRSGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNITLFLRGCKELGLKESQLFDP 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 163310745  103 SDLQDTSNRVTVKSLDYSRKLKNVLVTIYWLGKAANSC 140
Cdd:cd21278    81 GDLQDTSNRVTIKSSDCSRKLKNVLITIYWLGKAANSC 118

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 163310745    986 CSSCGLPLGkGAAMIIETLNLYFHIQCFRCGICKGQLgdavSGTDVRIRNGLLNCNDC 1043
Cdd:smart00132    2 CAGCGKPIY-GTERVLRALGKVWHPECFKCATCGKPL----SGDTFFEKDGKLYCKDC 54

calponin homology (CH) domain found in LIM and calponin homology domains-containing protein 1; LIM and calponin homology domains-containing protein 1 (LIMCH1) acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. LIMCH1 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   23 AFSEAQKWIEQVTGRSFGDKDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDP 102
Cdd:cd21278     1 AFTEAQKWIEQVTGRSFGDKDFRSGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNITLFLRGCKELGLKESQLFDP 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 163310745  103 SDLQDTSNRVTVKSLDYSRKLKNVLVTIYWLGKAANSC 140
Cdd:cd21278    81 GDLQDTSNRVTIKSSDCSRKLKNVLITIYWLGKAANSC 118

Calponin homology domain; Actin binding domains present in duplicate at the N-termini of spectrin-like proteins (including dystrophin, alpha-actinin). These domains cross-link actin filaments into bundles and networks. A calponin homology domain is predicted in yeasst Cdc24p.

                            10        20        30        40        50        60        70        80
                    ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745     26 EAQKWIEQVTGRSFGDK--DFRTGLENGILLCELLNAIKPGLV--KKINRLPTPIAGLDNIILFLRGCKELGLKEsQLFD 101
Cdd:smart00033    2 TLLRWVNSLLAEYDKPPvtNFSSDLKDGVALCALLNSLSPGLVdkKKVAASLSRFKKIENINLALSFAEKLGGKV-VLFE 80

                    ....*.
gi 163310745    102 PSDLQD 107
Cdd:smart00033   81 PEDLVE 86

Zinc-binding domain present in Lin-11, Isl-1, Mec-3; Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

                            10        20        30        40        50
                    ....*....|....*....|....*....|....*....|....*....|....*...
gi 163310745    986 CSSCGLPLGkGAAMIIETLNLYFHIQCFRCGICKGQLgdavSGTDVRIRNGLLNCNDC 1043
Cdd:smart00132    2 CAGCGKPIY-GTERVLRALGKVWHPECFKCATCGKPL----SGDTFFEKDGKLYCKDC 54

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

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 163310745   986 CSSCGLPlgkgaamIIET-----LNLYFHIQCFRCGICKGQLGDavsgTDVRIRNGLLNCNDCYMRSR 1048
Cdd:pfam00412    1 CAGCNRP-------IYDRelvraLGKVWHPECFRCAVCGKPLTT----GDFYEKDGKLYCKHDYYKLF 57

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 163310745  770 EEERRRQEKWQQEQERLLQERYQKEQDKLKEEWEKAQK 807
Cdd:cd16269   218 EEQQRELEQKLEDQERSYEEHLRQLKEKMEEERENLLK 255

calponin homology (CH) domain found in LIM and calponin homology domains-containing protein 1; LIM and calponin homology domains-containing protein 1 (LIMCH1) acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. LIMCH1 contains a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   23 AFSEAQKWIEQVTGRSFGDKDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDP 102
Cdd:cd21278     1 AFTEAQKWIEQVTGRSFGDKDFRSGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNITLFLRGCKELGLKESQLFDP 80

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 163310745  103 SDLQDTSNRVTVKSLDYSRKLKNVLVTIYWLGKAANSC 140
Cdd:cd21278    81 GDLQDTSNRVTIKSSDCSRKLKNVLITIYWLGKAANSC 118

calponin homology (CH) domain found in LIM domain only protein 7 and similar proteins; This family includes LIM domain only protein 7 (LMO-7) and LIM and calponin homology domains-containing protein 1 (LIMCH1), and similar proteins. LMO-7, also called F-box only protein 20, or LOMP, is a transcription regulator for expression of many Emery-Dreifuss muscular dystrophy (EDMD)-relevant genes. It binds to alpha-actinin and AF6/afadin at adherens junctions for epithelial cell-cell adhesion. LIMCH1 acts as an actin stress fiber-associated protein that activates the non-muscle myosin IIa complex by promoting the phosphorylation of its regulatory subunit MRLC/MYL9. It positively regulates actin stress fiber assembly and stabilizes focal adhesions, and therefore negatively regulates cell spreading and cell migration. Members of this family contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   23 AFSEAQKWIEQVTGRSFGDKDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDP 102
Cdd:cd21208     1 ALKEARTWIEAVTGKKFPSDDFRESLEDGILLCELINAIKPGSIKKINRLPTPIAGLDNLNLFLKACEDLGLKDSQLFDP 80

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 163310745  103 SDLQDTSNRVT---VKSLDYSRKLKNVLVTIYWLGKAAN 138
Cdd:cd21208    81 TDLQDLSNRRIathVRKKEDERRLKNVAITLYWLGRAAR 119

calponin homology (CH) domain superfamily; CH domains are actin filament (F-actin) binding motifs, which may be present as a single copy or in tandem repeats (which increase binding affinity). They either function as autonomous actin binding motifs or serve a regulatory function. CH domains are found in cytoskeletal and signal transduction proteins, including actin-binding proteins like spectrin, alpha-actinin, dystrophin, utrophin, and fimbrin, as well as proteins essential for regulation of cell shape (cortexillins), and signaling proteins (Vav).

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   25 SEAQKWIEQVTGRSFGD--KDFRTGLENGILLCELLNAIKPGLVKKINRLP-TPIAGLDNIILFLRGCKELGLKESQLFD 101
Cdd:cd00014     2 EELLKWINEVLGEELPVsiTDLFESLRDGVLLCKLINKLSPGSIPKINKKPkSPFKKRENINLFLNACKKLGLPELDLFE 81

                          90       100       110
                  ....*....|....*....|....*....|....
gi 163310745  102 PSDLQDTSNrvtvksldysrkLKNVLVTIYWLGK 135
Cdd:cd00014    82 PEDLYEKGN------------LKKVLGTLWALAL 103

calponin homology (CH) domain found in the calponin family; Calponin is an actin filament-associated regulatory protein expressed in smooth muscle and many types of non-muscle cells. There are three calponin isoforms, calponin-1, -2, -3. All of them are actin-binding proteins with functions in inhibiting actin-activated myosin ATPase and stabilizing the actin cytoskeleton. Calponin-1 is specifically expressed in smooth muscle cells and plays a role in fine-tuning smooth muscle contractility. Calponin-2 is expressed in both smooth muscle and non-muscle cells and regulates multiple actin cytoskeleton-based functions. Calponin-3 is expressed in the brain and participates in actin cytoskeleton-based activities in embryonic development and myogenesis. Members of this family contain a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   25 SEAQKWIEQVTGRSFGDkDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDPSD 104
Cdd:cd21211     6 AELRTWIEGVTGLSIGP-NFQKGLKDGIILCELINKLQPGSVKKINESMQNWHQLENIGNFIKAIVSYGMKPHDIFEAND 84

                          90
                  ....*....|..
gi 163310745  105 LQDTSNRVTVKS 116
Cdd:cd21211    85 LFENGNMTQVQV 96

calponin homology (CH) domain found in calponin-2; Calponin-2 (CNN2), also called neutral calponin, or smooth muscle calponin H2, is an actin cytoskeleton-associated regulatory protein that inhibits the activity of myosin-ATPase and cytoskeleton dynamics. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   25 SEAQKWIEQVTGRSFGDkDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDPSD 104
Cdd:cd21283     6 AELRTWIEGLTGRSIGP-DFQKGLKDGVILCELMNKLQPGSVPKINRSMQNWHQLENLSNFIKAMVSYGMKPVDLFEAND 84

                          90
                  ....*....|.
gi 163310745  105 LQDTSNRVTVK 115
Cdd:cd21283    85 LFESGNMTQVQ 95

calponin homology (CH) domain found in calponin-3; Calponin-3 (CNN3), also called acidic isoform calponin, is an F-actin-binding protein that is expressed in the brain and has been shown to control dendritic spine morphology, density, and plasticity by regulating actin cytoskeletal reorganization and dynamics. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   26 EAQKWIEQVTGRSFGDkDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDPSDL 105
Cdd:cd21284     9 ELRNWIEEVTGMSIGE-NFQKGLKDGVILCELINKLQPGSIRKINESKLNWHQLENIGNFIKAIQAYGMKPHDIFEANDL 87

                          90
                  ....*....|.
gi 163310745  106 QDTSNRVTVKS 116
Cdd:cd21284    88 FENGNMTQVQT 98

Calponin homology (CH) domain; The CH domain is found in both cytoskeletal proteins and signal transduction proteins. The CH domain is involved in actin binding in some members of the family. However in calponins there is evidence that the CH domain is not involved in its actin binding activity. Most member proteins have from two to four copies of the CH domain, however some proteins such as calponin have only a single copy.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745    29 KWIEQVTGRSFGD---KDFRTGLENGILLCELLNAIKPGLVKKINRLPTPIAGLDNIILFLRGC-KELGLKEsQLFDPSD 104
Cdd:pfam00307    9 RWINSHLAEYGPGvrvTNFTTDLRDGLALCALLNKLAPGLVDKKKLNKSEFDKLENINLALDVAeKKLGVPK-VLIEPED 87

                           90       100       110
                   ....*....|....*....|....*....|....*
gi 163310745   105 LqdtsnrvtvksldYSRKLKNVLVTIYWLGKAANS 139
Cdd:pfam00307   88 L-------------VEGDNKSVLTYLASLFRRFQA 109

calponin homology (CH) domain found in the IQ motif containing GTPase activating protein family; Members of the IQ motif containing GTPase activating protein (IQGAP) family are associated with the Ras GTP-binding protein and act as essential regulators of cytoskeletal function. There are three known IQGAP family members: IQGAP1, IQGAP2, and IQGAP3. They are multi-domain molecules having a calponin-homology (CH) domain which binds F-actin, IQGAP-specific repeats, a single WW domain, four IQ motifs that mediate interactions with calmodulin, and a RasGAP related domain that binds active Rho family GTPases. IQGAP1 negatively regulates Ras family GTPases by stimulating their intrinsic GTPase activity. It lacks GAP activity. Both IQGAP1 and IQGAP2 specifically bind to Cdc42 and Rac1, but not to RhoA. Despite similarities to part of the sequence of RasGAP, neither IQGAP1 nor IQGAP2 interacts with Ras. IQGAP3 regulates the organization of the cytoskeleton under the regulation of Rac1 and Cdc42 in neuronal cells. The depletion of IQGAP3 is shown to impair neurite or axon outgrowth in neuronal cells with disorganized cytoskeleton.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   26 EAQKWIEQVTGRSFGD-KDFRTGLENGILLCELLNAIKPGLVKKINrlpTPIAGL-----DNIILFLRGCKELGLKESQL 99
Cdd:cd21206    12 EAKQWIEACLNEELPPtTEFEEELRNGVVLAKLANKFAPKLVPLKK---IYDVGLqfrhtDNINHFLRALKKIGLPKIFH 88

                          90
                  ....*....|.
gi 163310745  100 FDPSDLQDTSN 110
Cdd:cd21206    89 FETTDLYEKKN 99

calponin homology (CH) domain found in the Pak Interactive eXchange factor family; Pak Interactive eXchange factor (PIX) proteins are Rho guanine nucleotide exchange factors (GEFs), which activate small GTPases by exchanging bound GDP for free GTP. They act as GEFs for both Cdc42 and Rac1, and have been implicated in cell motility, adhesion, neurite outgrowth, and cell polarity. Vertebrates contain two proteins from the PIX family, alpha-PIX and beta-PIX. Alpha-PIX, also called Rho guanine nucleotide exchange factor 6 (ARHGEF6), is localized in dendritic spines where it regulates spine morphogenesis. It controls dendritic length and spine density in the hippocampus. Mutations in the ARHGEF6 gene cause X-linked intellectual disability in humans. Beta-PIX, also called Rho guanine nucleotide exchange factor 7 (ARHGEF7), plays important roles in regulating neuroendocrine exocytosis, focal adhesion maturation, cell migration, synaptic vesicle localization, and insulin secretion. Both alpha-PIX and beta-PIX contain a single copy of the CH domain at the N-terminus. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   45 RTGLENGILLCELLNAIKPGLVKKINRLPTPIAG-LDNIILFLRGCKELGLKESQLFDPSDLQDTSNrvtvksldysrkL 123
Cdd:cd21202    31 SESLKNGVVLCRLVNRLKPGTVEKIYDEPTTEEEcLYNFESFLKACQELGILAEEIFDPNDLYSGGN------------F 98

                          90
                  ....*....|....*.
gi 163310745  124 KNVLVTIYWLGKAANS 139
Cdd:cd21202    99 QKVLSTLERLEKVAGG 114

LIM is a small protein-protein interaction domain, containing two zinc fingers; LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] (where X denotes any amino acid).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 163310745  986 CSSCGLPLGkgAAMIIETLNLYFHIQCFRCGICKGQLGdavsGTDVRIRNGLLNCNDCY 1044
Cdd:cd08368     1 CAGCGKPIE--GRELLRALGKKWHPECFKCAECGKPLG----GDSFYEKDGKPYCEKCY 53

calponin homology (CH) domain found in the growth arrest-specific protein 2 family; The growth arrest-specific protein 2 (GAS-2) family includes GAS-2, and GAS-2 like proteins, GAS2L1-3. GAS-2 may play a role in apoptosis by acting as a cell death substrate for caspases. GAS2L1 (also called GAS2-related protein on chromosome 22 or growth arrest-specific protein 2-like 1) and GAS2L2 (also called GAS2-related protein on chromosome 17 or growth arrest-specific protein 2-like 2) may be involved in the cross-linking of microtubules and microfilaments. GAS2L3, also called GAS2-like protein 3, is a cytoskeletal linker protein that may promote and stabilize the formation of the actin and microtubule network. Members of this family contain a single copy of the CH domain at the N-terminal region. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   30 WIEQVtgrsFGDKD----FRTGLENGILLCELLNAI--------------KPGLVKKI----NRLPTPIAGLDNIILFLR 87
Cdd:cd21204    14 WLNDL----LGDDLtpdnFLDELRNGVVLCQLAQKIqeaaekareagkknGPPPSYKLkcneNAKPGSFFARDNVANFLR 89

                          90
                  ....*....|....*...
gi 163310745   88 GCKELGLKESQLFDPSDL 105
Cdd:cd21204    90 WCRKLGVDEVLLFESEDL 107

calponin homology (CH) domain found in VAV3 protein and similar proteins; VAV3 is ubiquitously expressed and functions as a phosphorylation-dependent guanine nucleotide exchange factor (GEF) for RhoA, RhoG, and Rac1. Its function has been implicated in the hematopoietic, bone, cerebellar, and cardiovascular systems. VAV3 is essential in axon guidance in neurons that control blood pressure and respiration. It is overexpressed in prostate cancer cells and it plays a role in regulating androgen receptor transcriptional activity. VAV proteins contain several domains that enable their function: N-terminal calponin homology (CH), acidic, RhoGEF (also called Dbl-homologous or DH), Pleckstrin Homology (PH), C1 (zinc finger), SH2, and two SH3 domains. The model corresponds to CH domain, an actin-binding domain which is present as a single copy in VAV3 protein.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   43 DFRTGLENGILLCELLNAIKPGLV--KKINRLP--TPIAGLDNIILFLRG-CKELGLKESQLFDPSDLQD 107
Cdd:cd21264    31 DLAQTLRDGVLLCQLLNNLRPHSInlKEINLRPqmSQFLCLKNIRTFLSAcCETFGMRKSELFEAFDLFD 100

Calponin [Cytoskeleton];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   26 EAQKWIEQVTGRSFGDK-DFRTGLENGILLCELLNAIKPGLVK-KINRLPtpIAGLDNIILFLRGCKELGLKESQLFDPS 103
Cdd:COG5199    17 EVTLWIETVLGEKFEPPgDLLSLLKDGVRLCRILNEASPLDIKyKESKMP--FVQMENISSFINGLKKLRVPEYELFQTN 94

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 163310745  104 DLQDtsnrvtvksldySRKLKNVLVTIYWLGKAAN 138
Cdd:COG5199    95 DLFE------------AKDLRQVVICLYSLSRYAQ 117

Protein involved in regulation of cellular morphogenesis/cytokinesis [Cell division and chromosome partitioning / Signal transduction mechanisms];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   25 SEAQKWIEQVTGRSFGDKDFRTGLENGILLCELLNAIKPGLVKKI---NRLptPIAGLDNIILFLRGCKELGLKESQLFD 101
Cdd:COG5261    47 SEAKIWIEEVIEEALPELCFEDSLRNGVFLAKLTQRFNPDLTTVIfpaDKL--QFRHTDNINAFLDLIEHVGLPESFHFE 124

                          90
                  ....*....|...
gi 163310745  102 PSDLQDTSNRVTV 114
Cdd:COG5261   125 LQDLYEKKNIPKV 137

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.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 163310745  986 CSSCGLPL----GKGAAMIIETLNLYFHIQCFRCGICKGQLGDAVSGTDVRIRNGLLNCNDC 1043
Cdd:cd09357     1 CSVCGEPImpepGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCKSC 62

calponin homology (CH) domain found in the leucine-rich repeat and calponin homology domain-containing protein family; The leucine-rich repeat and calponin homology domain-containing protein (LRCH) family includes LRCH1-4. LRCH1, also called calponin homology domain-containing protein 1, or neuronal protein 81 (NP81), acts as a negative regulator of GTPase Cdc42 by sequestering Cdc42-guanine exchange factor DOCK8. LRCH2 may play a role in the organization of the cytoskeleton. LRCH3 is part of the DISP complex and may regulate the association of septins with actin and thereby regulate the actin cytoskeleton. LRCH4, also called leucine-rich repeat neuronal protein 4, or leucine-rich neuronal protein, acts as a novel Toll-like receptor (TLR) accessory protein that regulates the innate immune response. Members of this family contain a single copy of the CH domain at the C-terminus. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 163310745   48 LENGILLCELLNAIKPGLVKKINRLP------TPIAGLDNIILFLRGCKELGLKESQLFDPSDLQDTSN--RV--TVKSL 117
Cdd:cd21205    26 LMDGVVLCHLANHVRPRSVPSIHVPSpavpklSMAKCRRNVENFLEACRKLGVPEERLCSPGDILEEKGlvRVavTVQAL 105

calponin homology (CH) domain found in transgelin-2; Transgelin-2, also called epididymis tissue protein Li 7e, or SM22-alpha homolog, acts as an actin-binding protein that induces actin gelation and regulates the actin cytoskeleton. It may participate in the development and progression of multiple cancers. It contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 163310745   40 GDKDFRTGLENGILLCELLNAIKP---GLVKKINRLPTPIAGLDNIILFLRGCKELGLKESQLFDPSDLQDTSNRVTVK 115
Cdd:cd21280    31 GRENFQNWLKDGTVLCHLINSLYPkgqAPVKKIQASTMAFKQMEQISQFLQAAERYGINTTDIFQTVDLWEGKNMASVQ 109

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.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 163310745  986 CSSCGLPLGKGAAMIiETLNLYFHIQCFRCGICKGQL 1022
Cdd:cd09461     1 CVSCGFPIEAGDRWV-EALNNNYHSQCFNCTRCNVNL 36

Guanylate-binding protein, C-terminal domain; Guanylate-binding protein (GBP), C-terminal domain. Guanylate-binding proteins (GBPs) are synthesized after activation of the cell by interferons. The biochemical properties of GBPs are clearly different from those of Ras-like and heterotrimeric GTP-binding proteins. They bind guanine nucleotides with low affinity (micromolar range), are stable in their absence, and have a high turnover GTPase. In addition to binding GDP/GTP, they have the unique ability to bind GMP with equal affinity and hydrolyze GTP not only to GDP, but also to GMP. This C-terminal domain has been shown to mediate inhibition of endothelial cell proliferation by inflammatory cytokines.

                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 163310745  770 EEERRRQEKWQQEQERLLQERYQKEQDKLKEEWEKAQK 807
Cdd:cd16269   218 EEQQRELEQKLEDQERSYEEHLRQLKEKMEEERENLLK 255

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 163310745  986 CSSCGLPLGKGAAmiIETLNLYFHIQCFRCGICKGQLGdavSGTDVRI-RNGLLNCNDC 1043
Cdd:cd09394     1 CVGCKESITEGHA--YELGGDRWHIHCFKCYKCDKKLS---CDSNFLVlGDGSLICSDC 54

The second LIM domain of protein PINCH; The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 163310745  986 CSSCG-LPLGKgaamIIETLNLYFHIQCFRCGICKGQLGD 1024
Cdd:cd09332     1 CGKCGeFVIGR----VIKAMNNNWHPDCFRCEICNKELAD 36