Bivalent Mical/EHBP Rab binding domain; A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907112930 683 EMDNIERQLDALEHSGVLLEEKLRG-GANEGSEDDMLVDWFKLIHEKHLLVRRESELIYVFKQQNLEQRQADVEFELRCL 761
Cdd:pfam12130   1 ELEEIEERQRELEERGVELEKALRGeMSGDEEEEQLLQEWFKLVNEKNALVRRESELMYLAKEQDLEERQARLEQELREL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907112930 762 LNKPEKDWTDEDRAREKVLMQELMTLIEQRDAIVNCLDEDRQR 804
Cdd:pfam12130  81 MSKPDWLKTEEDKQREEELLEELVEIVEQRDALVDSLEEDRLR 123

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSGPEEGTFVCAERC 191
Cdd:cd09444     1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

Bivalent Mical/EHBP Rab binding domain; A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907112930 683 EMDNIERQLDALEHSGVLLEEKLRG-GANEGSEDDMLVDWFKLIHEKHLLVRRESELIYVFKQQNLEQRQADVEFELRCL 761
Cdd:pfam12130   1 ELEEIEERQRELEERGVELEKALRGeMSGDEEEEQLLQEWFKLVNEKNALVRRESELMYLAKEQDLEERQARLEQELREL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907112930 762 LNKPEKDWTDEDRAREKVLMQELMTLIEQRDAIVNCLDEDRQR 804
Cdd:pfam12130  81 MSKPDWLKTEEDKQREEELLEELVEIVEQRDALVDSLEEDRLR 123

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSGPEEGTFVCAERC 191
Cdd:cd09444     1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907112930  25 SLSKENVFENNRLAFEVAEKELGIP-ALLDPNDMVSmsvPDCLSIMTYVSQYYNHF 79
Cdd:pfam00307  55 NKSEFDKLENINLALDVAEKKLGVPkVLIEPEDLVE---GDNKSVLTYLASLFRRF 107

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

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVCaERC 191
Cdd:pfam00412   1 CAGCNRPIYDRELVRALGKVWHPECFRCAVCGKPLTTGDFYE--KDGKLYC-KHD 52

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
                   ....*....|....*....|....*....|....*....|....*....|.
gi 1907112930   25 SLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSvPDCLSIMTYVSQY 75
Cdd:smart00033  52 SLSRFKKIENINLALSFAEKLGGKVVLFEPEDLVEGP-KLILGVIWTLISL 101

Bivalent Mical/EHBP Rab binding domain; A variety of different effector proteins interact specifically with GTP-bound Rab proteins and mediate their versatile roles in membrane trafficking, including budding of vesicles from a donor membrane, directed transport through the cell and finally tethering and fusion with a target membrane. The 'bivalent Mical/EHBP Rab binding' (bMERB) domain is a Rab effector domain that is present in proteins of the Mical and EHBP families, both known to act in endosomal trafficking. The bMERB domain displays a preference for Rab8 family proteins (Rab8, 10, 13 and 15) and at least some of the bMERB domains contain two separate binding sites for Rab-proteins, allowing Micals and EHBPs to bind two Rabs simultaneously. The strong similarity between the two binding sites within one bMRB domain strongly suggests an evolutionarily development via duplication of a common ancestor supersecondary structure element. The bMERB domain has a completely alpha-helical fold consisting of a central helix and N- and C-terminal helices folding back on this central helix.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907112930 683 EMDNIERQLDALEHSGVLLEEKLRG-GANEGSEDDMLVDWFKLIHEKHLLVRRESELIYVFKQQNLEQRQADVEFELRCL 761
Cdd:pfam12130   1 ELEEIEERQRELEERGVELEKALRGeMSGDEEEEQLLQEWFKLVNEKNALVRRESELMYLAKEQDLEERQARLEQELREL 80

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1907112930 762 LNKPEKDWTDEDRAREKVLMQELMTLIEQRDAIVNCLDEDRQR 804
Cdd:pfam12130  81 MSKPDWLKTEEDKQREEELLEELVEIVEQRDALVDSLEEDRLR 123

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.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSGPEEGTFVCAERC 191
Cdd:cd09444     1 CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHF 79
Cdd:cd21197    47 DFHSLKKDNWLENNRLAFRVAETSLGIPALLDAEDMVTMHVPDRLSIITYVSQYYNHF 104

calponin homology (CH) domain found in the EH domain-binding protein (EHBP) family; The EHBP family includes EHBP1 and EHBP1-like protein (EHBP1L1). 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. EHBP1L1 may also act as Rab effector protein and play a role in vesicle trafficking. It coordinates Rab8 and Bin1 to regulate apical-directed transport in polarized epithelial cells. 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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKeLGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHFT 80
Cdd:cd21198    48 DFSSLSPHDIKENCKLAFDAAAK-LGIPRLLDPADMVLLSVPDKLSVMTYLHQIRAHFT 105

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        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVC 187
Cdd:cd09358     1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYAS--LEGKLYC 49

second calponin homology (CH) domain found in the beta spectrin family; The beta spectrin family includes beta-I, -II, -III, -IV and -V spectrins. 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. Beta-I spectrin, also called spectrin beta chain, erythrocytic (SPTB), may be involved in anaemia pathogenesis. Beta-II spectrin, also called spectrin beta chain, non-erythrocytic 1 (SPTBN1), or fodrin beta chain, is a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. Beta-IV spectrin is also called spectrin, non-erythroid beta chain 3 (SPTBN3) or spectrin beta chain, non-erythrocytic 4 (SPTBN4). Its mutation associates with congenital myopathy, neuropathy, and central deafness. Beta-III spectrin is also called spectrin beta chain, non-erythrocytic 2 (SPTBN2), or spinocerebellar ataxia 5 protein (SCA5). Beta-V spectrin, also called spectrin beta chain, non-erythrocytic 5 (SPTBN5), is a mammalian ortholog of Drosophila beta H spectrin. Beta-III and Beta-V spectrins may play crucial roles as longer actin-membrane cross-linkers or fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. 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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDmVSMSVPDCLSIMTYVSQYYNHF 79
Cdd:cd21194    49 DYNRLDPNDHLGNLNNAFDVAEQELGIAKLLDAED-VDVARPDEKSIMTYVASYYHYF 105

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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHF 79
Cdd:cd21195    51 NFDSLNEDDAVENNQLAFDVAEREFGIPPVTTGKEMASAQEPDKLSMVMYLSKFYELF 108

second calponin homology (CH) domain found in synaptic nuclear envelope protein 1 (SYNE-1) and similar proteins; 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, is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-1 also acts as a component of the LINC (LInker of Nucleoskeleton and Cytoskeleton) complex, which is involved in the connection between the nuclear lamina and the cytoskeleton. SYNE-1 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
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDmVSMSVPDCLSIMTYVSQYYNHF 79
Cdd:cd21243    52 DMESLKRRSNRENLETAFTVAEKELGIPRLLDPED-VDVDKPDEKSIMTYVAQFLKKY 108

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930  21 SDFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVpDCLSIMTYVSQY 75
Cdd:cd21184    45 PDNESLDKENPLENATKAMDIAEEELGIPKIITPEDMVSPNV-DELSVMTYLSYF 98

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).

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgPEEGTFVCaERC 191
Cdd:cd09400     5 CASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYE-TEYGSYCC-ETC 57

calponin homology (CH) domain found in molecule interacting with CasL protein 3; MICAL-3 is 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-3 seems to act as a Rab effector protein and plays a role in vesicle trafficking. It is involved in exocytic vesicle tethering and fusion. MICAL3 contains a single copy of the CH domain. CH domains are actin filament (F-actin) binding motifs.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHF 79
Cdd:cd21251    52 DFDSLDEQDVEKNNQLAFDIAEKEFGISPIMTGKEMASVGEPDKLSMVMYLTQFYEMF 109

The first Lim domain of pollen specific protein SF3; The first Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVC 187
Cdd:cd09440     5 CKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSS--MEGVLYC 53

second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 2 (SPTBN2) 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. SPTBN2, also called beta-III spectrin, or spinocerebellar ataxia 5 protein (SCA5), probably plays an important role in the neuronal membrane skeleton. Mutations in SPTBN2 is associated with spinocerebellar ataxia type 5. SPTBN2 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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDmVSMSVPDCLSIMTYVSQYYNHFT 80
Cdd:cd21321    52 DFETLKKSNAHYNLQNAFNVAEKELGLTKLLDPED-VNVDQPDEKSIITYVATYYHYFS 109

second calponin homology (CH) domain found in spectrin beta chain, erythrocytic (SPTB) 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. SPTB, also called beta-I spectrin, may be involved in anaemia pathogenesis. SPTB 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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSvPDCLSIMTYVSQYYNHFT 80
Cdd:cd21319    52 DFGKLKKSNARHNLEHAFNVAERQLGITKLLDPEDVFTEN-PDEKSIITYVVAFYHYFS 109

calponin homology (CH) domain found in the smoothelin family; The smoothelin family includes smoothelin and smoothelin-like proteins. Smoothelins are actin-binding cytoskeletal proteins that are abundantly expressed in healthy visceral (smoothelin-A) and vascular (smoothelin-B) smooth muscle. 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. SMTNL2 is highly expressed in skeletal muscle and could be associated with differentiating myocytes. 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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMS-VPDCLSIMTYVSQYYNHF 79
Cdd:cd21200    48 DYSSLDPKNRRKNFELAFSTAEELADIAPLLEVEDMVRMGnRPDWKCVFTYVQSLYRHL 106

second calponin homology (CH) domain found in alpha-actinin-2; Alpha-actinin-2 (ACTN2), also called alpha-actinin skeletal muscle isoform 2, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. ACTN2 is a bundling protein. Its mutations are associated with cardiomyopathies, as well as skeletal muscle disorder. 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHFTSSGQAAAS 88
Cdd:cd21288    57 DYSKLNKDDPIGNINLAMEIAEKHLDIPKMLDAEDIVNTPKPDERAIMTYVSCFYHAFAGAEQAETA 123

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 1907112930  137 CAACGQRVHLVQRYL-AEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVCaERC 191
Cdd:smart00132   2 CAGCGKPIYGTERVLrALGKVWHPECFKCATCGKPLSGDTFFE--KDGKLYC-KDC 54

second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 1 (SPTBN1) 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. SPTBN1, also called beta-II spectrin, fodrin beta chain, or spectrin, non-erythroid beta chain 1, is also a component of fodrin, which is the general spectrin-like protein that seems to be involved in secretion. Fodrin interacts with calmodulin in a calcium-dependent manner and is thus a candidate for the calcium-dependent movement of the cytoskeleton at the membrane. SPTBN1 contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

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gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDmVSMSVPDCLSIMTYVSQYYNHFT 80
Cdd:cd21320    49 DFDKLKKSNAHYNLQNAFNLAEQHLGLTKLLDPED-ISVDHPDEKSIITYVVTYYHYFS 106

second calponin homology (CH) domain found in alpha-actinin-1; Alpha-actinin-1 (ACTN1), also called alpha-actinin cytoskeletal isoform, or non-muscle alpha-actinin-1, is an F-actin cross-linking protein which is thought to anchor actin to a variety of intracellular structures. ACTN1 is a bundling protein. Its mutations cause congenital macrothrombocytopenia. 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.

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gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHFTSSGQ 84
Cdd:cd21287    57 DYGKLRKDDPLTNLNTAFDVAEKYLDIPKMLDAEDIVGTARPDEKAIMTYVSSFYHAFSGAQK 119

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.

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                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVC 187
Cdd:cd09445     1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQS--HEGNLYC 49

The LIM domains of thymus LIM protein (TLP); The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

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                  ....*....|....*....|....*....|....*....|.
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYS 177
Cdd:cd09401     1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHS 41

second calponin homology (CH) domain found in filamins; 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. Members of this family contain two copies of the CH domain. The model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

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gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVpDCLSIMTYVSQY 75
Cdd:cd21230    46 DWETWDPNDALENATEAMQLAEDWLGVPQLITPEEIINPNV-DEMSVMTYLSQF 98

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).

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gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVCaERC 191
Cdd:cd08368     1 CAGCGKPIEGRELLRALGKKWHPECFKCAECGKPLGGDSFYE--KDGKPYC-EKC 52

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.

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gi 1907112930 137 CAACGQRV---HLVQRylAEGRLYHRHCFRCRQCSSTLVPG 174
Cdd:cd09387     1 CSACGQSIpasELVMR--AQGNVYHLKCFTCSTCHNQLVPG 39

second calponin homology (CH) domain found in plectin and similar proteins; 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 can also bind muscle proteins such as actin to membrane complexes in muscle. Plectin contains two copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

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gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDmVSMSVPDCLSIMTYVSQYYN 77
Cdd:cd21238    49 DMNKVYRQTNLENLDQAFSVAERDLGVTRLLDPED-VDVPQPDEKSIITYVSSLYD 103

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

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                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907112930 137 CAACGQRVHLVQRYLAEGRLYHRHCFRCRQCSSTLVPGSYSSgpEEGTFVCaERC 191
Cdd:pfam00412   1 CAGCNRPIYDRELVRALGKVWHPECFRCAVCGKPLTTGDFYE--KDGKLYC-KHD 52

second calponin homology (CH) domain found in Drosophila melanogaster protein jitterbug and similar proteins; Protein jitterbug (Jbug) is an actin-meshwork organizing protein. It is required to maintain the shape and cell orientation of the Drosophila notum epithelium during flight muscle attachment to tendon cells. Jbug contains three copies of the CH domain. This model corresponds to the second CH domain. CH domains are actin filament (F-actin) binding motifs.

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gi 1907112930  21 SDFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDMVSMSVpDCLSIMTYVSQYYNH 78
Cdd:cd21229    47 PNWRKLDPSNSLENCRRAMDLAKREFNIPMVLSPEDLSSPHL-DELSGMTYLSYFMKE 103

second calponin homology (CH) domain found in the dystrophin family; The dystrophin family includes dystrophin and its paralog, utrophin. 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. Dystrophin is also involved in maintaining the structural integrity of cells, as well as in the formation of the blood-brain barrier (BBB). Utrophin, also called dystrophin-related protein 1 (DRP-1), is an autosomal dystrophin homolog that increases dystrophic muscle function and reduces pathology. It is broadly expressed in both the mRNA and protein levels, and occurs in the cerebrovascular endothelium. Utrophin forms the utrophin-glycoprotein complex (UGC) by interacting with dystroglycans (DGs) and sarcoglycan-dystroglycans, as well as sarcoglycan and sarcospan (SG-SSPN) subcomplexes. It may act as a scaffolding protein that stabilizes lipid microdomains and clusters mechanosensitive channel subunits, and link the F-actin cytoskeleton to the cell membrane via the associated glycoprotein complex. 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.

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gi 1907112930  22 DFQSLSKENVFENNRLAFEVAEKELGIPALLDPNDmVSMSVPDCLSIMTYVSQYY 76
Cdd:cd21187    47 DFDSLVKDSPESRLEHAFTVAHEHLGIEKLLDPED-VNVEQPDKKSILMYVTSLF 100

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907112930  23 FQSLSKENVFENNRLAFEVAEkELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHF 79
Cdd:cd21257    56 YQELSSQDKKRNLLLAFQAAE-SVGIKPSLELSEMMYTDRPDWQSVMQYVAQIYKYF 111

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.

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gi 1907112930  23 FQSLSKENVFENNRLAFEVAEkELGIPALLDPNDMVSMSVPDCLSIMTYVSQYYNHFTS 81
Cdd:cd21256    62 YQELNSQDKRRNFTLAFQAAE-SVGIKSTLDINEMVRTERPDWQSVMTYVTAIYKYFET 119