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        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYAFDRDDpqGRFYCTQHF 1130
Cdd:cd09439    1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDD--GKFYCKPHF 55

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

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  567 TLLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQS 646
Cdd:cd22198    4 ELLSWCQEQTEGYRGV-KVTDLTSSWRSGLALCAIIHRFRPDLIDFSSLDPENIAENNQLAFDVAEQELGIPPVMTGQEM 82

                         90       100
                 ....*....|....*....|...
gi 28573119  647 LDLTELESRIWLNYLDQICDLFR 669
Cdd:cd22198   83 ASLAVPDKLSMVSYLSQFYEAFK 105

transport protein TonB; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  1430 AAIAAGQKVTPTPSATA-----PGLQPKSkfdEKFEKVVSP-----PQPVVEPKPKPVidfnldELKPRKPNFEERPKEQ 1499
Cdd:PRK10819   56 ADLEPPQAVQPPPEPVVepepePEPIPEP---PKEAPVVIPkpepkPKPKPKPKPKPV------KKVEEQPKREVKPVEP 126

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 28573119  1500 LPrPESLKKPPQQKPKgSSTNVSRSNSLKSNASNGsPK 1537
Cdd:PRK10819  127 RP-ASPFENTAPARPT-SSTATAAASKPVTSVSSG-PR 161

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYAFDRDDpqGRFYCTQHF 1130
Cdd:cd09439    1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDD--GKFYCKPHF 55

calponin homology (CH) domain found in the MICAL and EHBP families; This group is composed of the molecule interacting with CasL protein (MICAL) and EH domain-binding protein (EHBP) families. 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. 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. EHBP proteins contain a single CH domain. CH domains are actin filament (F-actin) binding motifs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  567 TLLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQS 646
Cdd:cd22198    4 ELLSWCQEQTEGYRGV-KVTDLTSSWRSGLALCAIIHRFRPDLIDFSSLDPENIAENNQLAFDVAEQELGIPPVMTGQEM 82

                         90       100
                 ....*....|....*....|...
gi 28573119  647 LDLTELESRIWLNYLDQICDLFR 669
Cdd:cd22198   83 ASLAVPDKLSMVSYLSQFYEAFK 105

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28573119    567 TLLRWISAQLHSYQFIPELKEASDVFRNGRVLCALINRYRPDLIDYA--ATKDMSPVECNELSFAVLERELHIDRVM 641
Cdd:pfam00307    6 ELLRWINSHLAEYGPGVRVTNFTTDLRDGLALCALLNKLAPGLVDKKklNKSEFDKLENINLALDVAEKKLGVPKVL 82

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
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119     567 TLLRWISAQLHSYQFIPeLKEASDVFRNGRVLCALINRYRPDLIDYAA-TKDMSPVECNE 625
Cdd:smart00033    2 TLLRWVNSLLAEYDKPP-VTNFSSDLKDGVALCALLNSLSPGLVDKKKvAASLSRFKKIE 60

putative bacillithiol system oxidoreductase, YpdA family; Members of this protein family, including YpdA from Bacillus subtilis, are apparent oxidoreductases present only in species with an active bacillithiol system. They have been suggested actually to be thiol disulfide oxidoreductases (TDOR), although the evidence is incomplete. [Unknown function, Enzymes of unknown specificity]

                           10        20
                   ....*....|....*....|....*....
gi 28573119    130 VLVIGAGPCGLRTAIEAQLLGAKVVVLEK 158
Cdd:TIGR04018    2 VIIIGAGPCGLACAIEAQKAGLSYLIIEK 30

FAD binding domain; This family includes members that bind FAD. This family includes the flavoprotein subunits from succinate and fumarate dehydrogenase, aspartate oxidase and the alpha subunit of adenylylsulphate reductase.

                           10        20
                   ....*....|....*....|....*....
gi 28573119    130 VLVIGAGPCGLRTAIEAQLLGAKVVVLEK 158
Cdd:pfam00890    2 VLVIGGGLAGLAAALAAAEAGLKVAVVEK 30

transport protein TonB; Provisional

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  1430 AAIAAGQKVTPTPSATA-----PGLQPKSkfdEKFEKVVSP-----PQPVVEPKPKPVidfnldELKPRKPNFEERPKEQ 1499
Cdd:PRK10819   56 ADLEPPQAVQPPPEPVVepepePEPIPEP---PKEAPVVIPkpepkPKPKPKPKPKPV------KKVEEQPKREVKPVEP 126

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 28573119  1500 LPrPESLKKPPQQKPKgSSTNVSRSNSLKSNASNGsPK 1537
Cdd:PRK10819  127 RP-ASPFENTAPARPT-SSTATAAASKPVTSVSSG-PR 161

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        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYAFDRDDpqGRFYCTQHF 1130
Cdd:cd09439    1 CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDD--GKFYCKPHF 55

calponin homology (CH) domain found in the MICAL and EHBP families; This group is composed of the molecule interacting with CasL protein (MICAL) and EH domain-binding protein (EHBP) families. 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. 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. EHBP proteins contain a single CH domain. CH domains are actin filament (F-actin) binding motifs.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  567 TLLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQS 646
Cdd:cd22198    4 ELLSWCQEQTEGYRGV-KVTDLTSSWRSGLALCAIIHRFRPDLIDFSSLDPENIAENNQLAFDVAEQELGIPPVMTGQEM 82

                         90       100
                 ....*....|....*....|...
gi 28573119  647 LDLTELESRIWLNYLDQICDLFR 669
Cdd:cd22198   83 ASLAVPDKLSMVSYLSQFYEAFK 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  558 SGDLLPqgATLLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHI 637
Cdd:cd21195    1 SGDIRP--SKLLTWCQQQTEGYQHV-NVTDLTTSWRSGLALCAIIHRFRPELINFDSLNEDDAVENNQLAFDVAEREFGI 77

                         90       100       110
                 ....*....|....*....|....*....|...
gi 28573119  638 DRVMSAKQSLDLTELESRIWLNYLDQICDLFRG 670
Cdd:cd21195   78 PPVTTGKEMASAQEPDKLSMVMYLSKFYELFRG 110

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins; The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. 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 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYAfdrdDPQGRFYCTQHF 1130
Cdd:cd09442    1 CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYA----SLHGRIYCKPHF 53

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 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQSL 647
Cdd:cd21250    9 LLTWCQKQTEGYQNV-NVTDLTTSWKSGLALCAIIHRFRPELIDFDSLNEDDAVKNNQLAFDVAEREFGIPPVTTGKEMA 87

                         90       100
                 ....*....|....*....|...
gi 28573119  648 DLTELESRIWLNYLDQICDLFRG 670
Cdd:cd21250   88 SAEEPDKLSMVMYLSKFYELFRG 110

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQSL 647
Cdd:cd21251   10 LLGWCQRQTEGYAGV-NVTDLTMSWKSGLALCAIIHRYRPDLIDFDSLDEQDVEKNNQLAFDIAEKEFGISPIMTGKEMA 88

                         90       100
                 ....*....|....*....|..
gi 28573119  648 DLTELESRIWLNYLDQICDLFR 669
Cdd:cd21251   89 SVGEPDKLSMVMYLTQFYEMFK 110

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 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYafdrDDPQGRFYCTQHF 1130
Cdd:cd09445    1 CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNY----QSHEGNLYCKVHF 53

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 28573119  128 TRVLVIGAGPCGLRTAIEAQLLGAKVVVLEKRDRI-TRNNVLHLWPFVITDLRNLGAK-------------KFYGKFCAG 193
Cdd:COG0654    4 TDVLIVGGGPAGLALALALARAGIRVTVVERAPPPrPDGRGIALSPRSLELLRRLGLWdrllargapirgiRVRDGSDGR 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  194 SIDHISI-------------RQLQCMLLKVALLLGVEIHEGVSFDhAVEPSGDGggwrAAVTPADHpvSHYEFDVLIGAD 260
Cdd:COG0654   84 VLARFDAaetglpaglvvprADLERALLEAARALGVELRFGTEVT-GLEQDADG----VTVTLADG--RTLRADLVVGAD 156

                 ...
gi 28573119  261 GKR 263
Cdd:COG0654  157 GAR 159

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
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28573119    567 TLLRWISAQLHSYQFIPELKEASDVFRNGRVLCALINRYRPDLIDYA--ATKDMSPVECNELSFAVLERELHIDRVM 641
Cdd:pfam00307    6 ELLRWINSHLAEYGPGVRVTNFTTDLRDGLALCALLNKLAPGLVDKKklNKSEFDKLENINLALDVAEKKLGVPKVL 82

calponin homology (CH) domain found in MICAL-like protein 2 and similar proteins; MICAL-like protein 2 (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 subfamily contain a single copy of CH domain. CH domains are actin filament (F-actin) binding motifs.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 28573119  592 FRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQSLDLTELESRIWLNYLDQICDLFR 669
Cdd:cd21253   29 WRDGLAFCAIIHRFRPDLIDFDSLSKENVYENNKLAFTVAEKELGIPALLDAEDMVALKVPDKLSILTYVSQYYNYFH 106

second calponin homology (CH) domain found in the alpha-actinin family; The alpha-actinin (ACTN) family includes alpha-actinin-1, -2, -3, and -4. They are F-actin cross-linking proteins which are thought to anchor actin to a variety of intracellular structures. ACTN1 mutations cause congenital macrothrombocytopenia. ACTN2 mutations are associated with cardiomyopathies, as well as skeletal muscle disorder. ACTN3 is critical in anchoring the myofibrillar actin filaments and plays a key role in muscle contraction. ACTN4 is associated with cell motility and cancer invasion. It is probably involved in vesicular trafficking via its association with the CART complex, which is necessary for efficient transferrin receptor recycling but not for epidermal growth factor receptor (EGFR) degradation. 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 28573119  592 FRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSA 643
Cdd:cd21216   38 WKDGLAFCALIHRHRPDLLDYDKLRKDDPRENLNLAFDVAEKHLDIPKMLDA 89

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVM 641
Cdd:cd21192    8 LLKWVQAEIGKYYGI-RVTDFDKSWRDGVAFLALIHAIRPDLVDMKTVKNRSPRDNLELAFRIAEQHLNIPRLL 80

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 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAkQSL 647
Cdd:cd21189    6 LLLWARRTTEGYPGV-RVTNFTSSWRDGLAFNAIIHRNRPDLIDFRSVRNQSNRENLENAFNVAEKEFGVTRLLDP-EDV 83

                         90       100
                 ....*....|....*....|.
gi 28573119  648 DLTELESRIWLNYLDQICDLF 668
Cdd:cd21189   84 DVPEPDEKSIITYVSSLYDVF 104

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 28573119    1073 KCRFCKQTVYLMEKT-TVEGLVLHRNCLKCHHCHTNLRLGGYAFDrddpQGRFYCTQH 1129
Cdd:smart00132    1 KCAGCGKPIYGTERVlRALGKVWHPECFKCATCGKPLSGDTFFEK----DGKLYCKDC 54

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
                    ....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119     567 TLLRWISAQLHSYQFIPeLKEASDVFRNGRVLCALINRYRPDLIDYAA-TKDMSPVECNE 625
Cdd:smart00033    2 TLLRWVNSLLAEYDKPP-VTNFSSDLKDGVALCALLNSLSPGLVDKKKvAASLSRFKKIE 60

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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAkQSL 647
Cdd:cd21194    7 LLLWCQRKTAGYPGV-NIQNFTTSWRDGLAFNALIHAHRPDLIDYNRLDPNDHLGNLNNAFDVAEQELGIAKLLDA-EDV 84

                         90
                 ....*....|....
gi 28573119  648 DLTELESRIWLNYL 661
Cdd:cd21194   85 DVARPDEKSIMTYV 98

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.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYAfDRDdpqGRFYCTQ 1128
Cdd:cd09401    1 CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHS-EHE---GKPYCNK 51

calponin homology (CH) domain found in EH domain-binding protein 1-like protein 1 and similar proteins; EHBP1L1 may 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 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 28573119  566 ATLLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLErELHIDRVMSAKQ 645
Cdd:cd21255    4 QSLLEWCQEVTAGYRGV-RVTNFTTSWRNGLAFCAILHHFHPDLVDYESLDPLDIKENNKKAFEAFA-SLGVPRLLEPAD 81

                         90       100
                 ....*....|....*....|...
gi 28573119  646 SLDLTELESRIWLNYLDQICDLF 668
Cdd:cd21255   82 MVLLPIPDKLIVMTYLCQLRAHF 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        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 28573119  563 PQGATLLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLErELHIDRVMS 642
Cdd:cd21198    1 SSGQDLLEWCQEVTKGYRGV-KITNLTTSWRNGLAFCAILHHFRPDLIDFSSLSPHDIKENCKLAFDAAA-KLGIPRLLD 78

                         90       100
                 ....*....|....*....|..
gi 28573119  643 AKQSLDLTELESRIWLNYLDQI 664
Cdd:cd21198   79 PADMVLLSVPDKLSVMTYLHQI 100

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 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATkDMSPVECN-ELSFAVLERELHIDRVMSAKQS 646
Cdd:cd21291   15 LLLWCQRKTAGYDEV-DVQDFTTSWTDGLAFCALIHRHRPDLIDYDKL-DKKDHRGNmQLAFDIASKEIGIPQLLDVEDV 92

                         90
                 ....*....|....*..
gi 28573119  647 LDLTELESRIWLNYLDQ 663
Cdd:cd21291   93 CDVAKPDERSIMTYVAY 109

putative bacillithiol system oxidoreductase, YpdA family; Members of this protein family, including YpdA from Bacillus subtilis, are apparent oxidoreductases present only in species with an active bacillithiol system. They have been suggested actually to be thiol disulfide oxidoreductases (TDOR), although the evidence is incomplete. [Unknown function, Enzymes of unknown specificity]

                           10        20
                   ....*....|....*....|....*....
gi 28573119    130 VLVIGAGPCGLRTAIEAQLLGAKVVVLEK 158
Cdd:TIGR04018    2 VIIIGAGPCGLACAIEAQKAGLSYLIIEK 30

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAK 644
Cdd:cd21249    9 LLIWCQRKTAGYTNV-NVQDFSRSWRDGLAFNALIHAHRPDLIDYGSLRPDRPLYNLANAFLVAEQELGISQLLDPE 84

second calponin homology (CH) domain found in the beta-I spectrin-like subfamily; The beta-I spectrin-like family includes beta-I, -II, -III and -IV 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-III spectrin, also called spectrin beta chain, non-erythrocytic 2 (SPTBN2), or spinocerebellar ataxia 5 protein (SCA5), may play a crucial role as a longer actin-membrane cross-linker or fulfill the need for greater extensible flexibility than can be provided by the other smaller conventional spectrins. 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. Members of this subfamily 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 28573119  593 RNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSA 643
Cdd:cd21248   31 RDGLAFNALIHKHRPDLIDYDKLSKSNALYNLQNAFNVAEQKLGLTKLLDP 81

The second LIM domain of thymus LIM protein (TLP); The second LIM domain of thymus LIM protein (TLP): 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. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 28573119 1074 CRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNLRLGGYAfdrdDPQGRFYC 1126
Cdd:cd09477    1 CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHA----EHDGSPYC 49

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVM 641
Cdd:cd21319   10 LLLWCQMKTAGYPNV-NVTNFTSSWKDGLAFNALIHKHRPDLVDFGKLKKSNARHNLEHAFNVAERQLGITKLL 82

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 28573119  568 LLRWISAQLHSYQFIpELKEASDVFRNGRVLCALINRYRPDLIDYAATKDMSPVECNELSFAVLERELHIDRVMSAKQSL 647
Cdd:cd21260    6 LLEWCRAKTRGYEHV-DIQNFSSSWSSGMAFCALIHKFFPDAFDYAELDPANRRHNFTLAFSTAEKHADCAPLLEVEDMV 84

                         90
                 ....*....|....*..
gi 28573119  648 DLTELESRIWLNYLDQI 664
Cdd:cd21260   85 RMSVPDSKCVYTYIQEL 101

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

                         10        20        30
                 ....*....|....*....|....*....|....*..
gi 28573119 1072 EKCRFCKQTVYLMEKTTVEGLVLHRNCLKCHHCHTNL 1108
Cdd:cd09479    1 KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNL 37