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
                  ....*....|....*....|....*....|....*....|....*.
gi 1907171801 764 CYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTLRLSAYAYDIED 809
Cdd:cd09439     1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDD 46

The LIM domain of Mical (molecule interacting with CasL); The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907171801 764 CYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTLRLSAYAYDIED 809
Cdd:cd09439     1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDD 46

Ca2+-binding actin-bundling protein fimbrin/plastin (EF-Hand superfamily) [Cytoskeleton];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 508 TTPKLTRNESVARSSKLLGWCQRQTEGY-SGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEK--NNQLAFD 584
Cdd:COG5069   114 TIATINEEGELTKHINLLLWCDEDTGGYkPEVDTFDFFRSWRDGLAFSALIHDSRPDTLDPNVLDLQKKNKalNNFQAFE 193

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1907171801 585 IAEKELGISPIMTGKEMASVGEPDKLSMVMYLTQFYEMF 623
Cdd:COG5069   194 NANKVIGIARLIGVEDIVNVSIPDERSIMTYVSWYIIRF 232

2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases [Coenzyme transport and metabolism, Energy production and conversion]; 2-polyprenyl-6-methoxyphenol hydroxylase and related FAD-dependent oxidoreductases is part of the Pathway/BioSystem: Ubiquinone biosynthesis

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801  85 TNTKCLIIGAGPCGLRTAIDLSLLGAKVVVIEKRDAFSRNN-VLHLWPFTIHDLRGLGAK-------------KFYGKFC 150
Cdd:COG0654     2 MRTDVLIVGGGPAGLALALALARAGIRVTVVERAPPPRPDGrGIALSPRSLELLRRLGLWdrllargapirgiRVRDGSD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 151 AGAIDHISI-------------RQLQLILLKVALILGIEIHVNVEFQGLVQPPEdqeneriGWRALVHPKThpvsEYEFE 217
Cdd:COG0654    82 GRVLARFDAaetglpaglvvprADLERALLEAARALGVELRFGTEVTGLEQDAD-------GVTVTLADGR----TLRAD 150

                  ....*....
gi 1907171801 218 VIIGGDGRR 226
Cdd:COG0654   151 LVVGADGAR 159

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
                   ....*....|....*....|....*....|....*....|..
gi 1907171801  764 CYFCQKRVYVMER-LSAEGKFFHRSCFKCEYCATTLRLSAYA 804
Cdd:smart00132   2 CAGCGKPIYGTERvLRALGKVWHPECFKCATCGKPLSGDTFF 43

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

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907171801 764 CYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTL 798
Cdd:pfam00412   1 CAGCNRPIYDRELVRALGKVWHPECFRCAVCGKPL 35

calponin homology (CH) domain found in molecule interacting with CasL protein 2 (MICAL-2), MICAL-3, and similar proteins; Molecule interacting with CasL protein (MICAL) is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase (MO) domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semaphorin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM and CH domains mediate interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein MO is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL functions to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL is also called junctional Rab13-binding protein (JRAB). Members of this family, which includes MICAL-2, MICAL-3, and similar proteins, contain one CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 516 ESVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPI 595
Cdd:cd21195     1 SGDIRPSKLLTWCQQQTEGYQHVNVTDLTTSWRSGLALCAIIHRFRPELINFDSLNEDDAVENNQLAFDVAEREFGIPPV 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 1907171801 596 MTGKEMASVGEPDKLSMVMYLTQFYEMFKD 625
Cdd:cd21195    81 TTGKEMASAQEPDKLSMVMYLSKFYELFRG 110

calponin homology (CH) domain found in molecule interacting with CasL protein 2; MICAL-2 is a nuclear [F-actin]-monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). MICAL-2 acts as a key regulator of the serum response factor (SRF) signaling pathway elicited by nerve growth factor and serum. It mediates oxidation and subsequent depolymerization of nuclear actin, leading to the increased MKL1/MRTF-A presence in the nucleus, promoting SRF:MKL1/MRTF-A-dependent gene transcription. MICAL-2 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 1907171801 516 ESVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPI 595
Cdd:cd21250     1 ESDIRPNKLLTWCQKQTEGYQNVNVTDLTTSWKSGLALCAIIHRFRPELIDFDSLNEDDAVKNNQLAFDVAEREFGIPPV 80

                          90       100
                  ....*....|....*....|....*....
gi 1907171801 596 MTGKEMASVGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21250    81 TTGKEMASAEEPDKLSMVMYLSKFYELFR 109

calponin homology (CH) domain found in the MICAL-like protein family; The MICAL-L family includes MICAL-L1 and MICAL-L2. MICAL-L1, also called molecule interacting with Rab13 (MIRab13), is a probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. It is a tubular endosomal membrane hub that connects Rab35 and Arf6 with Rab8a. It may be involved in a late step of receptor-mediated endocytosis regulating endocytosed-EGF receptor trafficking. Alternatively, it may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. MICAL-L1 may indirectly play a role in neurite outgrowth. MICAL-L2, also called junctional Rab13-binding protein (JRAB), or molecule interacting with CasL-like 2, acts as an effector of small Rab GTPases which is involved in junctional complexes assembly through the regulation of cell adhesion molecule transport to the plasma membrane, and actin cytoskeleton reorganization. It regulates the endocytic recycling of occludins, claudins, and E-cadherin to the plasma membrane and may thereby regulate the establishment of tight junctions and adherens junctions. Members of this family contain a single copy of CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEMAS 603
Cdd:cd21197     5 LLRWCRRQCEGYPGVNITNLTSSFRDGLAFCAILHRHRPELIDFHSLKKDNWLENNRLAFRVAETSLGIPALLDAEDMVT 84

                          90       100
                  ....*....|....*....|.
gi 1907171801 604 VGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21197    85 MHVPDRLSIITYVSQYYNHFR 105

calponin homology (CH) domain found in MICAL-like protein 1; MICAL-like protein 1 (MICAL-L1), also called molecule interacting with Rab13 (MIRab13), is a probable lipid-binding protein with higher affinity for phosphatidic acid, a lipid enriched in recycling endosome membranes. It is a tubular endosomal membrane hub that connects Rab35 and Arf6 with Rab8a. It may be involved in a late step of receptor-mediated endocytosis regulating endocytosed-EGF receptor trafficking. Alternatively, it may regulate slow endocytic recycling of endocytosed proteins back to the plasma membrane. MICAL-L1 may indirectly play a role in neurite outgrowth. 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 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEMAS 603
Cdd:cd21252     5 LQAWCRRQCEGYPGVEIRDLSSSFRDGLAFCAILHRHRPDLIDFDSLSKDNVYENNRLAFEVAERELGIPALLDPEDMVS 84

                          90       100
                  ....*....|....*....|...
gi 1907171801 604 VGEPDKLSMVMYLTQFYEMFKDS 626
Cdd:cd21252    85 MKVPDCLSIMTYVSQYYNHFSNP 107

second calponin homology (CH) domain found in Schizosaccharomyces pombe alpha-actinin-like protein 1 and similar proteins; Schizosaccharomyces pombe alpha-actinin-like protein 1 (SpAIN1) binds to actin and is involved in actin-ring formation and organization. It plays a role in cytokinesis and is involved in septation. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEMAS 603
Cdd:cd21291    15 LLLWCQRKTAGYDEVDVQDFTTSWTDGLAFCALIHRHRPDLIDYDKLDKKDHRGNMQLAFDIASKEIGIPQLLDVEDVCD 94

                          90       100
                  ....*....|....*....|
gi 1907171801 604 VGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21291    95 VAKPDERSIMTYVAYYFHAF 114

calponin homology (CH) domain found in EH domain-binding protein 1 and similar proteins; EHBP1 is a regulator of endocytic recycling and may play a role in actin reorganization by linking clathrin-mediated endocytosis to the actin cytoskeleton. It may act as an effector of small GTPases, including RAB-10 (Rab10), and play a role in vesicle trafficking. EHBP1 is associated with aggressive prostate cancer and insulin-stimulated trafficking and cell migration. Members of this subfamily 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 1907171801 521 SSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKeLGISPIMTGKE 600
Cdd:cd21254     3 SQSLLAWCKEVTKGYRGVKITNFTTSWRNGLAFCAILHHFRPDLIDYKSLNPHDIKENNKKAYDGFAS-LGISRLLEPSD 81

                          90       100
                  ....*....|....*....|...
gi 1907171801 601 MASVGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21254    82 MVLLAVPDKLTVMTYLYQIRAHF 104

second calponin homology (CH) domain found in the plectin/dystonin/MACF1 family; This family includes plectin, dystonin and microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 (MACF1). Plectin, also called PCN, PLTN, hemidesmosomal protein 1 (HD1), or plectin-1, is a structural component of muscle. It interlinks intermediate filaments with microtubules and microfilaments, and anchors intermediate filaments to desmosomes or hemidesmosomes. It could also bind muscle proteins such as actin to membrane complexes in muscle. Dystonin, also called 230 kDa bullous pemphigoid antigen, 230/240 kDa bullous pemphigoid antigen, bullous pemphigoid antigen 1 (BPA or BPAG1), dystonia musculorum protein, or hemidesmosomal plaque protein, is a cytoskeletal linker protein that acts as an integrator of intermediate filaments, actin, and microtubule cytoskeleton networks. It is required for anchoring either intermediate filaments to the actin cytoskeleton in neural and muscle cells, or keratin-containing intermediate filaments to hemidesmosomes in epithelial cells. MACF1, also called 620 kDa actin-binding protein (ABP620), actin cross-linking family protein 7 (ACF7), macrophin-1, or trabeculin-alpha, is a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. It facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 523 KLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTgKEMA 602
Cdd:cd21189     5 ALLLWARRTTEGYPGVRVTNFTSSWRDGLAFNAIIHRNRPDLIDFRSVRNQSNRENLENAFNVAEKEFGVTRLLD-PEDV 83

                          90       100
                  ....*....|....*....|.
gi 1907171801 603 SVGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21189    84 DVPEPDEKSIITYVSSLYDVF 104

second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 5 (SPTBN5) and similar proteins; Spectrin is an actin crosslinking and molecular scaffold protein that links the plasma membrane to the actin cytoskeleton, and functions in the determination of cell shape, arrangement of transmembrane proteins, and organization of organelles. It is composed of two antiparallel dimers of alpha- and beta- subunits. SPTBN5, also called beta-V spectrin, is a mammalian ortholog of Drosophila beta H spectrin that may play a crucial role as a longer actin-membrane cross-linker or to fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. SPTBN5 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 520 RSSK--LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMT 597
Cdd:cd21249     3 RSAKeaLLIWCQRKTAGYTNVNVQDFSRSWRDGLAFNALIHAHRPDLIDYGSLRPDRPLYNLANAFLVAEQELGISQLLD 82

                          90       100
                  ....*....|....*....|....*.
gi 1907171801 598 GKEMAsVGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21249    83 PEDVA-VPHPDERSIMTYVSLYYHYF 107

The LIM domain of Mical (molecule interacting with CasL); The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*.
gi 1907171801 764 CYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTLRLSAYAYDIED 809
Cdd:cd09439     1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDD 46

calponin homology (CH) domain found in the cytospin family; The cytospin family includes cytospin-A and cytospin-B. Cytospin-A, also called renal carcinoma antigen NY-REN-22, sperm antigen with calponin homology and coiled-coil domains 1-like, or SPECC1-like (SPECC1L) protein, is involved in cytokinesis and spindle organization. It may play a role in actin cytoskeleton organization and microtubule stabilization and hence, is required for proper cell adhesion and migration. Cytospin-B, also called nuclear structure protein 5 (NSP5), sperm antigen HCMOGT-1, or sperm antigen with calponin homology and coiled-coil domains 1 (SPECC1), is a novel fusion partner to PDGFRB in juvenile myelomonocytic leukemia with translocation t(5;17)(q33;p11.2). 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 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKeLGISPIMTGKEMAS 603
Cdd:cd21199    13 LLKWCQEKTQGYKGIDITNFSSSWNDGLAFCALLHSYLPDKIPYSELNPQDKRRNFTLAFKAAES-VGIPTTLTIDEMVS 91

                          90       100
                  ....*....|....*....|.
gi 1907171801 604 VGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21199    92 MERPDWQSVMSYVTAIYKHFE 112

second calponin homology (CH) domain found in the synaptic nuclear envelope protein (SYNE) family; The SYNE family includes SYNE-1, -2 and calmin. SYNE-1 (also called nesprin-1, enaptin, KASH domain-containing protein 1, KASH1, myocyte nuclear envelope protein 1, MYNE-1, or nuclear envelope spectrin repeat protein 1) and SYNE-2 (also called nesprin-2, KASH domain-containing protein 2, KASH2, nuclear envelope spectrin repeat protein 2, nucleus and actin connecting element protein, or protein NUANCE) may act redundantly. They are multi-isomeric modular proteins which form a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. They also act as components of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. Calmin, also called calponin-like transmembrane domain protein, is a protein with calponin homology (CH) and transmembrane domains expressed in maturing spermatogenic cells. It may be involved in the development and/or maintenance of neuronal functions. Members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEMaS 603
Cdd:cd21192     8 LLKWVQAEIGKYYGIRVTDFDKSWRDGVAFLALIHAIRPDLVDMKTVKNRSPRDNLELAFRIAEQHLNIPRLLEVEDV-L 86

                          90       100
                  ....*....|....*....|.
gi 1907171801 604 VGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21192    87 VDKPDERSIMTYVSQFLRMFP 107

calponin homology (CH) domain found in molecule interacting with CasL protein 1; MICAL-1, also called NEDD9-interacting protein with calponin homology and LIM domains, acts as a [F-actin]-monooxygenase that promotes depolymerization of F-actin by mediating oxidation of specific methionine residues on actin to form methionine-sulfoxide, resulting in actin filament disassembly and preventing repolymerization. In the absence of actin, it also functions as a NADPH oxidase producing H(2)O(2). MICAL-1 acts as a cytoskeletal regulator that connects NEDD9 to intermediate filaments. It also acts as a negative regulator of apoptosis via its interaction with STK38 and STK38L. MICAL-1 is a Rab effector protein that plays a role in vesicle trafficking. 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 1907171801 517 SVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIM 596
Cdd:cd21196     1 SSGTQEELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVV 80

                          90       100
                  ....*....|....*....|....*...
gi 1907171801 597 TGKemASVGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21196    81 SAQ--AVVAGSDPLGLIAYLSHFHSAFK 106

calponin homology (CH) domain found in cytospin-B; Cytospin-B, also called nuclear structure protein 5 (NSP5), or sperm antigen HCMOGT-1, or sperm antigen with calponin homology and coiled-coil domains 1 (SPECC1), is a novel fusion Cytospin-B that 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 1907171801 512 LTRNESVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEkELG 591
Cdd:cd21257     1 LAREYGGSKRNALLKWCQKKTEGYPNIDITNFSSSWSDGLAFCALLHTYLPAHIPYQELSSQDKKRNLLLAFQAAE-SVG 79

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907171801 592 ISPIMTGKEMASVGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21257    80 IKPSLELSEMMYTDRPDWQSVMQYVAQIYKYFE 112

second calponin homology (CH) domain found in the filamin family; The filamin family includes filamin-A (FLN-A), filamin-B (FLN-B) and filamin-C (FLN-C). Filamins function to anchor various transmembrane proteins to the actin cytoskeleton. FLN-A is also called actin-binding protein 280 (ABP-280), alpha-filamin, endothelial actin-binding protein, filamin-1, or non-muscle filamin. It promotes orthogonal branching of actin filaments and links actin filaments to membrane glycoproteins. It also serves as a scaffold for a wide range of cytoplasmic signaling proteins. FLN-B is also called ABP-278, ABP-280 homolog, actin-binding-like protein, beta-filamin, filamin homolog 1 (Fh1), filamin-3, thyroid autoantigen, truncated actin-binding protein, or truncated ABP. It connects cell membrane constituents to the actin cytoskeleton and may also promote orthogonal branching of actin filaments as well as link actin filaments to membrane glycoproteins. FLN-C, also called FLNc, ABP-280-like protein, ABP-L, actin-binding-like protein, filamin-2, or gamma-filamin, is a muscle-specific filamin that plays a central role in muscle cells, probably by functioning as a large actin-cross-linking protein. It may be involved in reorganizing the actin cytoskeleton in response to signaling events, and may also display structural functions at the Z lines in muscle cells. FLN-C is critical for normal myogenesis and for maintaining the structural integrity of the muscle fibers. This family also includes Drosophila melanogaster protein jitterbug (Jbug), which is an actin-meshwork organizing protein containing three copies of the CH domain. Other members of this family contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 522 SKLLGWCQRQTEGYsgvNVTDLTMSWKSGLALCAIIHRYRPDLI-DFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKE 600
Cdd:cd21184     4 SLLLEWVNSKIPEY---KVKNFTTDWNDGKALAALVDALKPGLIpDNESLDKENPLENATKAMDIAEEELGIPKIITPED 80

                          90
                  ....*....|....*....
gi 1907171801 601 MASvGEPDKLSMVMYLTQF 619
Cdd:cd21184    81 MVS-PNVDELSVMTYLSYF 98

second calponin homology (CH) domain found in alpha-actinin-3; Alpha-actinin-3 (ACTN3), also called alpha-actinin skeletal muscle isoform 3, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. ACTN3 is a bundling protein. It is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. It contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 516 ESVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPI 595
Cdd:cd21289     7 EETSAKEGLLLWCQRKTAPYRNVNVQNFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKM 86

                          90       100
                  ....*....|....*....|....*...
gi 1907171801 596 MTGKEMASVGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21289    87 LDAEDIVNTPKPDEKAIMTYVSCFYHAF 114

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 1907171801 524 LLGWCQRQTEGY-SGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEK--NNQLAFDIAEKELGISPI-MTGK 599
Cdd:pfam00307   7 LLRWINSHLAEYgPGVRVTNFTTDLRDGLALCALLNKLAPGLVDKKKLNKSEFDKleNINLALDVAEKKLGVPKVlIEPE 86

                          90       100
                  ....*....|....*....|....*
gi 1907171801 600 EMAsvgEPDKLSMVMYLTQFYEMFK 624
Cdd:pfam00307  87 DLV---EGDNKSVLTYLASLFRRFQ 108

second calponin homology (CH) domain found in cortexillin; Cortexillins are actin-bundling proteins that play a critical role in regulating cell morphology and actin cytoskeleton reorganization. They play a major role in cytokinesis and contain two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEMAS 603
Cdd:cd21226     5 LLAWCRQTTEGYDGVNITSFKSSFNDGRAFLALLHAYDPELFKQAAIEQMDAEARLNLAFDFAEKKLGIPKLLEAEDVMT 84

                          90       100
                  ....*....|....*....|
gi 1907171801 604 vGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21226    85 -GNPDERSIVLYTSLFYHAF 103

calponin homology (CH) domain found in smoothelin-like protein 1; Smoothelin-like protein 1 (SMTNL1), also called calponin homology-associated smooth muscle protein (CHASM), plays a role in the regulation of contractile properties of both striated and smooth muscles. It can bind to calmodulin and tropomyosin. When it is unphosphorylated, SMTNL1 may inhibit myosin dephosphorylation. SMTNL1 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 1907171801 522 SKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEM 601
Cdd:cd21260     4 NMLLEWCRAKTRGYEHVDIQNFSSSWSSGMAFCALIHKFFPDAFDYAELDPANRRHNFTLAFSTAEKHADCAPLLEVEDM 83

                          90
                  ....*....|....*....
gi 1907171801 602 ASVGEPDKLSMVMYLTQFY 620
Cdd:cd21260    84 VRMSVPDSKCVYTYIQELY 102

calponin homology (CH) domain found in cytospin-A; Cytospin-A, also called renal carcinoma antigen NY-REN-22, or sperm antigen with calponin homology and coiled-coil domains 1-like, or SPECC1-like protein (SPECC1L), is involved in cytokinesis and spindle organization. It may play a role in actin cytoskeleton organization and microtubule stabilization and hence, is required for proper cell adhesion and migration. Cytospin-A 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 1907171801 512 LTRNESVARSSKLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEkELG 591
Cdd:cd21256     7 LAREYGGSKRNALLKWCQKKTEGYQNIDITNFSSSWNDGLAFCALLHTYLPAHIPYQELNSQDKRRNFTLAFQAAE-SVG 85

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1907171801 592 ISPIMTGKEMASVGEPDKLSMVMYLTQFYEMFK 624
Cdd:cd21256    86 IKSTLDINEMVRTERPDWQSVMTYVTAIYKYFE 118

second calponin homology (CH) domain found in microtubule-actin cross-linking factor 1, isoforms 1/2/3/5 (MACF1) and similar proteins; MACF1, also called 620 kDa actin-binding protein (ABP620), actin cross-linking family protein 7 (ACF7), macrophin-1, or trabeculin-alpha, is a large protein containing numerous spectrin and leucine-rich repeat (LRR) domains. It facilitates actin-microtubule interactions at the cell periphery and couples the microtubule network to cellular junctions. MACF1 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 523 KLLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKeLGISPIMTGKEMa 602
Cdd:cd21240     8 KLLLWTQKVTAGYTGIKCTNFSSCWSDGKMFNALIHRYRPDLVDMERVQIQSNRENLEQAFEVAER-LGVTRLLDAEDV- 85

                          90       100
                  ....*....|....*....|.
gi 1907171801 603 SVGEPDKLSMVMYLTQFYEMF 623
Cdd:cd21240    86 DVPSPDEKSVITYVSSIYDAF 106

calponin homology (CH) domain found in smoothelin-B and similar proteins; Smoothelins are actin-binding cytoskeletal proteins that are abundantly expressed in healthy visceral (smoothelin-A) and vascular (smoothelin-B) smooth muscle. The human SMTN gene encodes smoothelin-A and smoothelin-B. This model corresponds to the single CH domain of smoothelin-B. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQNVEKNNQLAFDIAEKELGISPIMTGKEMAS 603
Cdd:cd21259     6 LLDWCRAKTRGYENVDIQNFSSSWSDGMAFCALVHNFFPEAFDYSQLSPQNRRHNFEVAFSSAEKHADCPQLLDVEDMVR 85

                          90
                  ....*....|....*..
gi 1907171801 604 VGEPDKLSMVMYLTQFY 620
Cdd:cd21259    86 MREPDWKCVYTYIQEFY 102

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.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1907171801 764 CYFCQKRVYVMERLSAEGKFFHRSCFKCEYCATTLRLSAYAYdIEDEF 811
Cdd:cd09358     1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYAS-LEGKL 47

second calponin homology (CH) domain found in dystrophin and similar proteins; Dystrophin, encoded by the DMD gene, is a large, submembrane cytoskeletal protein that is the main component of the dystrophin-glycoprotein complex (DGC) in skeletal muscles. It links the transmembrane DGC to the actin cytoskeleton through binding strongly to the cytoplasmic tail of beta-dystroglycan, the transmembrane subunit of a highly O-glycosylated cell-surface protein. It is involved in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Mutations in dystrophin lead to Duchenne muscular dystrophy (DMD). Moreover, dystrophin deficiency is associated with abnormal cerebral diffusion and perfusion, as well as in acute Trypanosoma cruzi infection. The dystrophin subfamily has been characterized by a compact cluster of domains comprising four EF-hand-like motifs and a ZZ-domain, followed by a looser region with two coiled-coils. These domains are believed to be involved in protein-protein interactions. In addition, dystrophin contains two syntrophin binding sites (SBSs) and a long N-terminal extension that comprises two actin-binding calponin homology (CH) domains, approximately 24 spectrin repeats (SRs) and a WW domain. The model corresponds to the second CH domain.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907171801 524 LLGWCQRQTEGYSGVNVTDLTMSWKSGLALCAIIHRYRPDLIDFDS-LDEQNVEKNNQLAFDIAEKELGISPIMTGKEMA 602
Cdd:cd21233     5 LLSWVRQSTRNYPQVNVINFTSSWSDGLAFNALIHSHRPDLFDWNSvVSQQSATERLDHAFNIARQHLGIEKLLDPEDVA 84