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 157822761  506 GSAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVL 585
Cdd:cd21196     1 SSGTQEELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVV 80

                          90       100
                  ....*....|....*....|....*.
gi 157822761  586 SAQAVVAGSDPLGLIAYLSHFHSAFK 611
Cdd:cd21196    81 SAQAVVAGSDPLGLIAYLSHFHSAFK 106

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 157822761  681 CELCGKRLYILERFCVDGHFFHRGCFCCRTCEATLRPGGYGQYPGDgyFYCLQH 734
Cdd:cd09358     1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGK--LYCKPH 52

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 157822761   83 TNTKCLVVGAGPCGLRAAVELALLGARVVLVEKRTKFSRHN-VLHLWPFTIHDLRALGAK-------------KFYGRFC 148
Cdd:COG0654     2 MRTDVLIVGGGPAGLALALALARAGIRVTVVERAPPPRPDGrGIALSPRSLELLRRLGLWdrllargapirgiRVRDGSD 81

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  149 TGTLDHISIRQLQLLLLKV-------------ALLLGVEIHWGFTFTGLQPppkKGSGWRARIqpsppAQLASYEFDVLI 215
Cdd:COG0654    82 GRVLARFDAAETGLPAGLVvpradleralleaARALGVELRFGTEVTGLEQ---DADGVTVTL-----ADGRTLRADLVV 153

                  ....*
gi 157822761  216 SAGGG 220
Cdd:COG0654   154 GADGA 158

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 157822761  506 GSAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVL 585
Cdd:cd21196     1 SSGTQEELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVV 80

                          90       100
                  ....*....|....*....|....*.
gi 157822761  586 SAQAVVAGSDPLGLIAYLSHFHSAFK 611
Cdd:cd21196    81 SAQAVVAGSDPLGLIAYLSHFHSAFK 106

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 157822761   511 EELLHWCQEQTAG-FPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSEL--QGMSALEATAWALRVAEYELGIIPVLS- 586
Cdd:pfam00307    5 KELLRWINSHLAEyGPGVRVTNFTTDLRDGLALCALLNKLAPGLVDKKKLnkSEFDKLENINLALDVAEKKLGVPKVLIe 84

                           90       100
                   ....*....|....*....|....*
gi 157822761   587 AQAVVAGsDPLGLIAYLSHFHSAFK 611
Cdd:pfam00307   85 PEDLVEG-DNKSVLTYLASLFRRFQ 108

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 157822761    511 EELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLE----PSELQGMSALEATAWALRVAEYELGIIPVLS 586
Cdd:smart00033    1 KTLLRWVNSLLAEYDKPPVTNFSSDLKDGVALCALLNSLSPGLVDkkkvAASLSRFKKIENINLALSFAEKLGGKVVLFE 80

                            90
                    ....*....|....*....
gi 157822761    587 AQAVVAGS-DPLGLIAYLS 604
Cdd:smart00033   81 PEDLVEGPkLILGVIWTLI 99

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 157822761    680 VCELCGKRLYILERFC-VDGHFFHRGCFCCRTCEATLRPGGYgqYPGDGYFYCLQH 734
Cdd:smart00132    1 KCAGCGKPIYGTERVLrALGKVWHPECFKCATCGKPLSGDTF--FEKDGKLYCKDC 54

FAD binding domain; This domain is involved in FAD binding in a number of enzymes.

                           10        20        30
                   ....*....|....*....|....*....|....*...
gi 157822761    85 TKCLVVGAGPCGLRAAVELALLGARVVLVEKRTKFSRH 122
Cdd:pfam01494    2 TDVLIVGGGPAGLMLALLLARAGVRVVLVERHATTSVL 39

Succinate dehydrogenase/fumarate reductase, flavoprotein subunit [Energy production and conversion]; Succinate dehydrogenase/fumarate reductase, flavoprotein subunit is part of the Pathway/BioSystem: TCA cycle

                          10        20
                  ....*....|....*....|....*...
gi 157822761   88 LVVGAGPCGLRAAVELALLGARVVLVEK 115
Cdd:COG1053     7 VVVGSGGAGLRAALEAAEAGLKVLVLEK 34

DNA double-strand break repair ATPase Rad50;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  906 EEEMKRFCKAQAIQRRLNEIEAAMRELETEgmKLEvalrKESSSPEKQKKLWLEQLLQLIQKKNSLVTEEAELMITVQEL 985
Cdd:PRK03918  358 EERHELYEEAKAKKEELERLKKRLTGLTPE--KLE----KELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEEL 431

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157822761  986 DLEEKQ-----RQLDHEFRG---------INR-EETLKTQADRLSEdrvLRKLLdvVNQRDALIQFQEERRLREM 1045
Cdd:PRK03918  432 KKAKGKcpvcgRELTEEHRKelleeytaeLKRiEKELKEIEEKERK---LRKEL--RELEKVLKKESELIKLKEL 501

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  902 RRAKEEEMKRFckaQAIQRRLNEIEAAMRELETEGMKLEValrkessspEKQKKLWLEQLLQLIQKKNSLVTEEAELMIT 981
Cdd:COG4717    80 LKEAEEKEEEY---AELQEELEELEEELEELEAELEELRE---------ELEKLEKLLQLLPLYQELEALEAELAELPER 147

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 157822761  982 VQELDLEEKQ-RQLDHEFRGINRE-ETLKTQADRLSEDRVLRKLLDVVNQRDALIQFQEERRLRE 1044
Cdd:COG4717   148 LEELEERLEElRELEEELEELEAElAELQEELEELLEQLSLATEEELQDLAEELEELQQRLAELE 212

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 157822761  506 GSAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVL 585
Cdd:cd21196     1 SSGTQEELLRWCQEQTAGYPGVHVSDLSSSWADGLALCALVYRLQPGLLEPSELQGLGALEATAWALKVAENELGITPVV 80

                          90       100
                  ....*....|....*....|....*.
gi 157822761  586 SAQAVVAGSDPLGLIAYLSHFHSAFK 611
Cdd:cd21196    81 SAQAVVAGSDPLGLIAYLSHFHSAFK 106

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 157822761   921 RLNEIEAAMRELETEGMKLEVALRKESSSPEKQKKLwLEQLLQLIQKKNSLVTEEAELMITVQELDLEEKQRQLDHEFRG 1000
Cdd:pfam12130    1 ELEEIEERQRELEERGVELEKALRGEMSGDEEEEQL-LQEWFKLVNEKNALVRRESELMYLAKEQDLEERQARLEQELRE 79

                           90       100       110       120
                   ....*....|....*....|....*....|....*....|....*.
gi 157822761  1001 I-NREETLKTQADRLSEDRVLRKLLDVVNQRDALIQFQEERRLREM 1045
Cdd:pfam12130   80 LmSKPDWLKTEEDKQREEELLEELVEIVEQRDALVDSLEEDRLREE 125

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 157822761  505 TGSAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPV 584
Cdd:cd21195     1 SGDIRPSKLLTWCQQQTEGYQHVNVTDLTTSWRSGLALCAIIHRFRPELINFDSLNEDDAVENNQLAFDVAEREFGIPPV 80

                          90       100       110
                  ....*....|....*....|....*....|
gi 157822761  585 LSAQAVVAGSDP--LGLIAYLSHFHSAFKN 612
Cdd:cd21195    81 TTGKEMASAQEPdkLSMVMYLSKFYELFRG 110

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 157822761  513 LLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAVVA 592
Cdd:cd21197     5 LLRWCRRQCEGYPGVNITNLTSSFRDGLAFCAILHRHRPELIDFHSLKKDNWLENNRLAFRVAETSLGIPALLDAEDMVT 84

                          90       100
                  ....*....|....*....|.
gi 157822761  593 GSDP--LGLIAYLSHFHSAFK 611
Cdd:cd21197    85 MHVPdrLSIITYVSQYYNHFR 105

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 157822761  511 EELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAV 590
Cdd:cd21189     4 EALLLWARRTTEGYPGVRVTNFTSSWRDGLAFNAIIHRNRPDLIDFRSVRNQSNRENLENAFNVAEKEFGVTRLLDPEDV 83

                          90       100
                  ....*....|....*....|.
gi 157822761  591 -VAGSDPLGLIAYLSHFHSAF 610
Cdd:cd21189    84 dVPEPDEKSIITYVSSLYDVF 104

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 157822761  513 LLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAVVA 592
Cdd:cd21252     5 LQAWCRRQCEGYPGVEIRDLSSSFRDGLAFCAILHRHRPDLIDFDSLSKDNVYENNRLAFEVAERELGIPALLDPEDMVS 84

                          90       100
                  ....*....|....*....|..
gi 157822761  593 GSDP--LGLIAYLSHFHSAFKN 612
Cdd:cd21252    85 MKVPdcLSIMTYVSQYYNHFSN 106

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 157822761  509 GTEELLHWCQEQtagFPGVSVTDFSSSWADGRALCALVHRLQPGLL-EPSELQGMSALEATAWALRVAEYELGIIPVLSA 587
Cdd:cd21184     2 GKSLLLEWVNSK---IPEYKVKNFTTDWNDGKALAALVDALKPGLIpDNESLDKENPLENATKAMDIAEEELGIPKIITP 78

                          90       100
                  ....*....|....*....|...
gi 157822761  588 QAVVAGS-DPLGLIAYLSHFHSA 609
Cdd:cd21184    79 EDMVSPNvDELSVMTYLSYFRNA 101

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 157822761  681 CELCGKRLYILERFCVDGHFFHRGCFCCRTCEATLRPGGYGQYPGDgyFYCLQH 734
Cdd:cd09358     1 CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGK--LYCKPH 52

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  511 EELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAV 590
Cdd:cd21319     8 DALLLWCQMKTAGYPNVNVTNFTSSWKDGLAFNALIHKHRPDLVDFGKLKKSNARHNLEHAFNVAERQLGITKLLDPEDV 87

                          90       100
                  ....*....|....*....|.
gi 157822761  591 -VAGSDPLGLIAYLSHFHSAF 610
Cdd:cd21319    88 fTENPDEKSIITYVVAFYHYF 108

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 157822761  511 EELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAV 590
Cdd:cd21249     7 EALLIWCQRKTAGYTNVNVQDFSRSWRDGLAFNALIHAHRPDLIDYGSLRPDRPLYNLANAFLVAEQELGISQLLDPEDV 86

                          90       100
                  ....*....|....*....|.
gi 157822761  591 -VAGSDPLGLIAYLSHFHSAF 610
Cdd:cd21249    87 aVPHPDERSIMTYVSLYYHYF 107

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 157822761  508 AGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEyELGIIPVLSA 587
Cdd:cd21240     4 SAKEKLLLWTQKVTAGYTGIKCTNFSSCWSDGKMFNALIHRYRPDLVDMERVQIQSNRENLEQAFEVAE-RLGVTRLLDA 82

                          90       100
                  ....*....|....*....|....
gi 157822761  588 QAV-VAGSDPLGLIAYLSHFHSAF 610
Cdd:cd21240    83 EDVdVPSPDEKSVITYVSSIYDAF 106

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  510 TEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEyELGIIPVLSAQA 589
Cdd:cd21198     3 GQDLLEWCQEVTKGYRGVKITNLTTSWRNGLAFCAILHHFRPDLIDFSSLSPHDIKENCKLAFDAAA-KLGIPRLLDPAD 81

                          90       100
                  ....*....|....*....|...
gi 157822761  590 VVAGS--DPLGLIAYL----SHF 606
Cdd:cd21198    82 MVLLSvpDKLSVMTYLhqirAHF 104

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  513 LLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAV-V 591
Cdd:cd21243    10 LLKWVQNAAAKRFGIEVKDFGPSWRDGVAFNAIIHSIRPDLVDMESLKRRSNRENLETAFTVAEKELGIPRLLDPEDVdV 89

                          90
                  ....*....|....*....
gi 157822761  592 AGSDPLGLIAYLSHFHSAF 610
Cdd:cd21243    90 DKPDEKSIMTYVAQFLKKY 108

second calponin homology (CH) domain found in synaptic nuclear envelope protein 2 (SYNE-2) and similar proteins; 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, is a multi-isomeric modular protein which forms a linking network between organelles and the actin cytoskeleton to maintain subcellular spatial organization. SYNE-2 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-2 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 157822761  513 LLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLSAQAV-V 591
Cdd:cd21244    10 LLLWAQEQCAKVGSISVTDFKSSWRNGLAFLAIIHALRPGLVDMEKLKGRSNRENLEEAFRIAEQELKIPRLLEPEDVdV 89

                          90       100
                  ....*....|....*....|
gi 157822761  592 AGSDPLGLIAYLSHFHSAFK 611
Cdd:cd21244    90 VNPDEKSIMTYVAQFLQYSK 109

second calponin homology (CH) domain found in spectrin beta chain, non-erythrocytic 4 (SPTBN4) 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. SPTBN4, also called beta-IV spectrin, or spectrin, non-erythroid beta chain 3 (SPTBN3), is a novel spectrin isolated as an interactor of the receptor tyrosine phosphatase-like protein ICA512. Its mutation associates with congenital myopathy, neuropathy, and central deafness. SPTBN4 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 157822761  494 KSDETDARKTTTGSagtEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALR 573
Cdd:cd21322     6 KIETEDNRETRSAK---DALLLWCQMKTAGYPEVNIQNFTTSWRDGLAFNALIHRHRPDLIDFSKLTKSNATYNLQQAFN 82

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 157822761  574 VAEYELGIIPVLSAQAV-VAGSDPLGLIAYLSHFHSAF 610
Cdd:cd21322    83 TAEQHLGLTKLLDPEDVnMEAPDEKSIITYVVSFYHYF 120

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        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  507 SAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLS 586
Cdd:cd21321     4 KSAKDALLLWCQMKTAGYPNVNVHNFTTSWRDGLAFNAIVHKHRPDLIDFETLKKSNAHYNLQNAFNVAEKELGLTKLLD 83

                          90       100
                  ....*....|....*....|....*
gi 157822761  587 AQAV-VAGSDPLGLIAYLSHFHSAF 610
Cdd:cd21321    84 PEDVnVDQPDEKSIITYVATYYHYF 108

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 157822761  507 SAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLS 586
Cdd:cd21289     9 TSAKEGLLLWCQRKTAPYRNVNVQNFHTSWKDGLALCALIHRHRPDLIDYAKLRKDDPIGNLNTAFEVAEKYLDIPKMLD 88

                          90       100
                  ....*....|....*....|....*.
gi 157822761  587 AQAVVAGSDP--LGLIAYLSHFHSAF 610
Cdd:cd21289    89 AEDIVNTPKPdeKAIMTYVSCFYHAF 114

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.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 157822761  507 SAGTEELLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQPGLLEPSELQGMSALEATAWALRVAEYELGIIPVLS 586
Cdd:cd21287     9 TSAKEGLLLWCQRKTAPYKNVNIQNFHISWKDGLGFCALIHRHRPELIDYGKLRKDDPLTNLNTAFDVAEKYLDIPKMLD 88

                          90       100
                  ....*....|....*....|....*.
gi 157822761  587 AQAVV--AGSDPLGLIAYLSHFHSAF 610
Cdd:cd21287    89 AEDIVgtARPDEKAIMTYVSSFYHAF 114

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
                  ....*....|....*....|....*....|....*....
gi 157822761  513 LLHWCQEQTAGFPGVSVTDFSSSWADGRALCALVHRLQP 551
Cdd:cd21200     6 LLEWCQAKTRGYEHVDITNFSSSWSDGMAFCALIHHFFP 44