first type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034569628  12 GVMNAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSVL 78
Cdd:cd22420    15 SMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSVL 81

SAM domain of BICC1 (bicaudal) subfamily; SAM (sterile alpha motif) domain of BICC1 (bicaudal) subfamily is a protein-protein interaction domain. Proteins of this group have N-terminal K homology RNA-binding vigilin-like repeats and a C-terminal SAM domain. BICC1 is involved in the regulation of embryonic differentiation. It plays a role in the regulation of Dvl (Dishevelled) signaling, particularly in the correct cilia orientation and nodal flow generation. In Drosophila, disruption of BICC1 can disturb the normal migration direction of the anterior follicle cell of oocytes; the specific function of SAM is to recruit whole protein to the periphery of P-bodies. In mammals, mutations in this gene are associated with polycystic kidney disease and it was suggested that the BICC1 protein can indirectly interact with ANKS6 protein (ANKS6 is also associated with polycystic kidney disease) through some protein and RNA intermediates.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628 824 SFKGSDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISELNKN 888
Cdd:cd09520     1 SAKYSDLPELLAKLGLEKYIDLFAQQEIDLQTFLTLTDQDLKELGITAFGARRKMLLAISELNKR 65

first type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034569628  12 GVMNAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSVL 78
Cdd:cd22420    15 SMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSVL 81

SAM domain of BICC1 (bicaudal) subfamily; SAM (sterile alpha motif) domain of BICC1 (bicaudal) subfamily is a protein-protein interaction domain. Proteins of this group have N-terminal K homology RNA-binding vigilin-like repeats and a C-terminal SAM domain. BICC1 is involved in the regulation of embryonic differentiation. It plays a role in the regulation of Dvl (Dishevelled) signaling, particularly in the correct cilia orientation and nodal flow generation. In Drosophila, disruption of BICC1 can disturb the normal migration direction of the anterior follicle cell of oocytes; the specific function of SAM is to recruit whole protein to the periphery of P-bodies. In mammals, mutations in this gene are associated with polycystic kidney disease and it was suggested that the BICC1 protein can indirectly interact with ANKS6 protein (ANKS6 is also associated with polycystic kidney disease) through some protein and RNA intermediates.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628 824 SFKGSDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISELNKN 888
Cdd:cd09520     1 SAKYSDLPELLAKLGLEKYIDLFAQQEIDLQTFLTLTDQDLKELGITAFGARRKMLLAISELNKR 65

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628  86 TLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNnqaEKSNQVSIAGQPAGVESARVRIRE 153
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESE---GNERIVTITGTPEAVEAAKALIEE 65

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034569628 238 STQLDIAAQHHLFMMGRNGSNIKHIMQRTGAQIHFPDPSNPQKKSTVYLQGTIESVCLARQYLM 301
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALIE 64

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034569628  236 PVSTQLDIAAQHHLFMMGRNGSNIKHIMQRTGAQIHFPDPSNPQKksTVYLQGTIESVCLARQYLMGCL 304
Cdd:smart00322   2 PVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGSEER--VVEITGPPENVEKAAELILEIL 68

K homology RNA-binding domain;

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*....
gi 1034569628   30 QKIMEETNTQIawpsklKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSVL 78
Cdd:smart00322  26 KKIEEETGVKI------DIPGPGSEERVVEITGPPENVEKAAELILEIL 68

first type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1034569628  12 GVMNAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSVL 78
Cdd:cd22420    15 SMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSVL 81

SAM domain of BICC1 (bicaudal) subfamily; SAM (sterile alpha motif) domain of BICC1 (bicaudal) subfamily is a protein-protein interaction domain. Proteins of this group have N-terminal K homology RNA-binding vigilin-like repeats and a C-terminal SAM domain. BICC1 is involved in the regulation of embryonic differentiation. It plays a role in the regulation of Dvl (Dishevelled) signaling, particularly in the correct cilia orientation and nodal flow generation. In Drosophila, disruption of BICC1 can disturb the normal migration direction of the anterior follicle cell of oocytes; the specific function of SAM is to recruit whole protein to the periphery of P-bodies. In mammals, mutations in this gene are associated with polycystic kidney disease and it was suggested that the BICC1 protein can indirectly interact with ANKS6 protein (ANKS6 is also associated with polycystic kidney disease) through some protein and RNA intermediates.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628 824 SFKGSDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISELNKN 888
Cdd:cd09520     1 SAKYSDLPELLAKLGLEKYIDLFAQQEIDLQTFLTLTDQDLKELGITAFGARRKMLLAISELNKR 65

SAM (Sterile alpha motif ); SAM (Sterile Alpha Motif) domain is a module consisting of approximately 70 amino acids. This domain is found in the Fungi/Metazoa group and in a restricted number of bacteria. Proteins with SAM domains are represented by a wide variety of domain architectures and have different intracellular localization, including nucleus, cytoplasm and membranes. SAM domains have diverse functions. They can interact with proteins, RNAs and membrane lipids, contain site of phosphorylation and/or kinase docking site, and play a role in protein homo and hetero dimerization/oligomerization in processes ranging from signal transduction to regulation of transcription. Mutations in SAM domains have been linked to several diseases.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1034569628 829 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISE 884
Cdd:cd09487     1 DVAEWLESLGLEQYADLFRKNEIDGDALLLLTDEDLKELGITSPGHRKKILRAIQR 56

SAM domain of ANKS6 (or SamCystin) subfamily; SAM (sterile alpha motif) domain of ANKS6 (or SamCystin) subfamily is a potential protein-protein interaction domain. Proteins of this subfamily have N-terminal ankyrin repeats and a C-terminal SAM domain. They are able to form self-associated complexes and both (SAM and ANK) domains play a role in such interactions. Mutations in Anks6 gene are associated with polycystic kidney disease. They cause formation of renal cysts in rodent models. It was suggested that the ANKS6 protein can interact indirectly (through RNA and protein intermediates) with BICC1, another polycystic kidney disease-associated protein.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628 829 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISELN 886
Cdd:cd09518     7 ELSGILRKLSLEKYQPIFEEQEVDMEAFLTLTDGDLKELGIKTDGPRQQILAAISELN 64

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628  86 TLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNnqaEKSNQVSIAGQPAGVESARVRIRE 153
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESE---GNERIVTITGTPEAVEAAKALIEE 65

SAM domain (Sterile alpha motif); It has been suggested that SAM is an evolutionarily conserved protein binding domain that is involved in the regulation of numerous developmental processes in diverse eukaryotes. The SAM domain can potentially function as a protein interaction module through its ability to homo- and heterooligomerise with other SAM domains.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628 828 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 885
Cdd:pfam00536   6 EDVGEWLESIGLGQYIDSFRAGYIDGDALLQLTEDDLLKLGVTLLGHRKKILYAIQRL 63

K homology (KH) RNA-binding domain, type I; KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include an N-terminal extension and type I KH domains (e.g. hnRNP K) contain a C-terminal extension. Some KH-I superfamily members contain a divergent KH domain that lacks the RNA-binding GXXG motif. Some others have a mutated GXXG motif which may or may not have nucleic acid binding ability.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034569628  87 LKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQaekSNQVSIAGQPAGVESARVRIR 152
Cdd:cd00105     1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSG---ERVVTITGTPEAVEKAKELIE 63

third type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034569628  85 VTLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSnrNNQAEKSNQVSIAGQPAGVESAR 148
Cdd:cd22422     2 VSMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDP--NNPPQRKSTVFISGSIDSVYLAR 63

SAM domain of sec23ip-like subfamily; SAM (sterile alpha motif) domain of Sec23ip-like (Sec23 interacting protein) subfamily is a potential protein-protein interaction domain. This group of proteins includes Sec23ip and DDHD2 proteins. All of them contain at least two domains: a SAM domain and a predicted metal-binding domain. For mammalian DDHD2 members of this group, phospholipase activity has been demonstrated. Sec23ip proteins of this group interact with Sec23 proteins via an N-terminal proline-rich region. Members of this subfamily are involved in organization of ER/Golgi intermediate compartment.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1034569628 826 KGSDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGItTFGARRKML 879
Cdd:cd09516     8 EPLTLEEDLEKLGLSEYFDTFEKEKIDMESLLLCSESDLKEMGI-PMGPRKKLL 60

SAM domain (Sterile alpha motif);

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1034569628 828 SDLPELFSKLGLGKYTDVFQQQEID-LQTFLTLTDQDLKELGITTFGARRKMLLAISEL 885
Cdd:pfam07647   7 ESVADWLRSIGLEQYTDNFRDQGITgAELLLRLTLEDLKRLGITSVGHRRKILKKIQEL 65

tenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the tenth one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628 238 STQLDIAA--QHHLFMMGRNGSNIKHIMQRTGAQIHFPdPSNPQKKSTVYLQGTIESVCLARQYL 300
Cdd:cd22413     2 SFTVEIRAkpEYHRFLIGRGGANIRKIRDNTGARIIFP-TARDEDQELITIIGTKEAVEKAKEEL 65

fourteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourteenth one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034569628  85 VTLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQaeksNQVSIAGQPAGVESARVRIRELL 155
Cdd:cd22417     1 FTLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDEND----DEITITGYEKNAEAAKDAILKIV 67

second type I K homology (KH) RNA-binding domain found in protein bicaudal C homolog 1 (BICC1) and similar proteins; BICC1, also called Bic-C, is a mammalian homologue of Drosophila Bicaudal-C (dBic-C). BICC1 functions as an RNA-binding protein that represses the translation of selected mRNAs to control development. It regulates gene expression and modulates cell proliferation and apoptosis. BICC1 is a negative regulator of Wnt signaling. Increased levels of BICC1 may be associated with depression. Besides, BICC1 is a genetic determinant of osteoblastogenesis and bone mineral density. BICC1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628 237 VSTQLDIAAQHHLFMMGRNGSNIKHIMQRTGAQIHFPDP--SNPQKKST-VYLQGTIESVCLARQ 298
Cdd:cd22421     3 VTLKMDVSHTDHSHVIGKGGNNIKKVMEDTGCHIHFPDSnrTSQAEKSNqVSIAGQPAGVESARA 67

SAM domain of USH1G_HARP family; SAM (sterile alpha motif) domain of USH1G/HARP (Usher syndrome type-1G/ Harmonin-interacting Ankyrin Repeat-containing protein) family is a protein-protein interaction domain. Members of this family have an N-terminal ankyrin repeat region and a C-terminal SAM domain. In mammals these proteins can interact via the SAM domain with the PDZ domain of harmonin to form a scaffolding complex that facilitates signal transduction in epithelial and inner ear sensory cells. It was suggested that USH1G and HARP can be tissue specific partners of harmonin. Mutations in ush1g genes lead to Usher syndrome type 1G. This syndrome is the cause of deaf-blindness in humans.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1034569628 827 GSDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGItTFGARRKMLLAISElnknRRKLFESP 896
Cdd:cd09517     2 TSPLERFLTSNHLEEYLPVFEREKIDLEALMLLTDEDLQSLKL-PLGPRRKLLNAIAK----RKQALENP 66

first type I K homology (KH) RNA-binding domain found in Saccharomyces cerevisiae Protein SCP160 and similar proteins; SCP160, also called protein HX, is a new yeast protein associated with the nuclear membrane and the endoplasmic reticulum. It is involved in the control of mitotic chromosome transmission. It is required during cell division for faithful partitioning of the ER-nuclear envelope membranes which enclose the duplicated chromosomes in yeast. SCP160 contains seven K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628  82 SNRVTLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNQA-----EKSNQVSIAGQPAGVESARVRI 151
Cdd:cd22446     4 SPKVTITISVPSSVRGAIIGSRGKNLKSIQDKTGTKIQIPKRNEEGNYdedddDETVEISIEGDAEGVELAKKEI 78

fifteenth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fifteenth one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1034569628  85 VTLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNNqaekSNQVSIAGQPAGVESAR 148
Cdd:cd22418     1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDAD----PNLVTITGLEENVEECK 60

third type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the third one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034569628 241 LDIAAQHHLFMMGRNGSNIKHIMQRTGAQIHFPDPSNpqKKSTVYLQGTIESVCLARQYLM 301
Cdd:cd22407     4 LDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSV--NKDEIVVSGEKEGVAQAVAKIK 62

fourth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the fourth one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1034569628  86 TLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNRNnqaekSNQVSIAGQPAGVESARVRI 151
Cdd:cd22408     1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSD-----SETITLRGPADKLGAALTLV 61

type I K homology (KH) RNA-binding domain found in Drosophila melanogaster eukaryotic translation initiation factor 4E-binding protein Mextli and similar proteins; Mextli is a novel eukaryotic translation initiation factor 4E-binding protein that promotes translation in Drosophila melanogaster.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628  99 VIGKGGNNIKKVMEETGCHIHF--PDSNRNNQaeksnQVSIAGQPAGVESARVRIREL 154
Cdd:cd22454    18 VIGKGGETIKRIEALTDTVITFerVNGGSPNR-----EVQITGSPDNVAAAKRLIEDT 70

sixth type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the sixth one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1034569628 236 PVSTQLDIAAQHHLFMMGRNGSNIKHIMQRTGAQIHFPDPSNPQkkSTVYLQGTIESVCLARQ 298
Cdd:cd02394     1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANS--DEIRIEGSPEGVKKAKA 61

SAM domain of sphingomyelin synthase related subfamily; SAM (sterile alpha motif) domain of SGMS-like (sphingomyelin synthase) subfamily is a potential protein-protein interaction domain. This group of proteins is related to sphingomyelin synthase 1, and contains an N-terminal SAM domain. The function of SGMS1-like proteins is unknown; they may play a role in sphingolipid metabolism.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1034569628 835 SKLGLGKYTDVF-QQQEIDLQTFLTLTDQDLKE--LGITTFGARRKMLLAISELNK 887
Cdd:cd09515    14 KKEGFSKYVDLLcNKHRIDGKVLLSLTEEDLRSppLEIKVLGDIKRLWLAIRKLQR 69

third type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628  99 VIGKGGNNIKKVMEETGCHIHF-PDsnRNNQAEKSNQVSiaGQPAGVESARVRIRELL 155
Cdd:cd22398    14 VIGKGGEMIKKIQNETGARVQFkPD--DGNSPDRICVIT--GPPDQVQHAARMIQELI 67

third type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1034569628 253 GRNGSNIKHIMQRTGAQIHFPDPSNPQKKSTVYLQGTIESVCLArQYL 300
Cdd:cd22439    18 GKGGTKINEIRQLSGATIKIANSEDGSTERSVTITGTPEAVSLA-QYL 64

SAM domain of Ste50_like (ubc2) subfamily; SAM (sterile alpha motif) domain of Ste50-like (or Ubc2 for Ustilago bypass of cyclase) subfamily is a putative protein-protein interaction domain. This group includes only fungal proteins. Basidiomycetes have an N-terminal SAM domain, central UBQ domain, and C-terminal SH3 domain, while Ascomycetes lack the SH3 domain. Ubc2 of Ustilago maydis is a major virulence and maize pathogenicity factor. It is required for filamentous growth (the budding haploid form of Ustilago maydis is a saprophyte, while filamentous dikaryotic form is a pathogen). Also the Ubc2 protein is involved in the pheromone-responsive morphogenesis via the MAP kinase cascade. The SAM domain is necessary for ubc2 function; deletion of SAM eliminates this function. A Lys-to-Glu mutation in the SAM domain of ubc2 gene induces temperature sensitivity.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1034569628 835 SKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 885
Cdd:cd09533     7 SSLGLPQYEDQFIENGITGDVLVALDHEDLKEMGITSVGHRLTILKAVYEL 57

second type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1034569628  99 VIGKGGNNIKKVMEETGCH-IHFPDSNRNNQAEKSnqVSIAGQPAGVESARVRIRELL 155
Cdd:cd22397    14 IIGKGGETIKQLQERAGVKmVMIQDGPQPTGQDKP--LRITGDPQKVQRAKELVMELI 69

SAM domain of tankyrase1,2 subfamily; SAM (sterile alpha motif) domain of Tankyrase1,2 subfamily is a protein-protein interaction domain. In addition to the SAM domain, proteins of this group have ankyrin repeats and a ADP- ribosyltransferase (poly-(ADP-ribose) synthase) domain. Tankyrases can polymerize through their SAM domains forming homoligomers and these complexes are disrupted by autoribosylation. Tankyrases apparently act as master scaffolding proteins and thus may interact simultaneously with multiple proteins, in particular with TRF1, NuMA, IRAP and Grb14 (ankyrin repeats are involved in these interactions). Tankyrases participate in a variety of cell signaling pathways as effector molecules. Their functions are different depending on the intracellular location: at telomeres they play a role in the regulation of telomere length via control of telomerase access to telomeres, at centrosomes they promote spindle assembly/disassembly, in Golgi vesicles they participate in the regulation of vesicle trafficking and Golgi dynamics. Tankyrase 1 may be of interest as new potential target for telomerase-directed cancer therapy.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1034569628 829 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 885
Cdd:cd09524     7 SISQFLSSLGLEHLREIFEREQITLDVLAEMGHEELKEIGINAYGHRHKLIKGVERL 63

SAM (Sterile alpha motif ); SAM (sterile alpha motif) domain of Smaug-like subfamily proteins is an RNA binding domain. SAM interacts with stem-loop structures in target mRNAs. Proteins of this subfamily are post-transcriptional regulators involved in mRNA silencing and deadenylation; they can be implicated in transcript stability regulation and vacuolar protein transport as well. SAM_Smaug-like domain-containing proteins are found in metazoa from yeast to human. In animals they are active during early embryogenesis.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1034569628 830 LPELFSKLGLGKYTDVFQQqeIDLQTFLTLTDQDLKELGITTFGARRKMLLAI 882
Cdd:cd09489     2 IPMWLKSLRLHKYSDAFKG--TTWEELLYLTEETLEKKGVLTLGARRKLLKAF 52

fourth type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the fourth one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1034569628  99 VIGKGGNNIKKVMEETGCHIHFpdsNRNNQAEKSNQV-SIAGQPAGVESARVRIRE 153
Cdd:cd22399    14 VIGKGGETIRQINQQSGAHVEL---DRNPPPNPNEKLfIIRGNPQQIEHAKQLIRE 66

SAM domain of caskin protein repeat 2; SAM (sterile alpha motif) domain repeat 2 of caskin1,2 proteins is a protein-protein interaction domain. Caskin has two tandem SAM domains. Caskin protein is known to interact with membrane-associated guanylate kinase CASK, and may play a role in neural development, synaptic protein targeting, and regulation of gene expression.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628 823 SSFKGSDLPELFSKLGLGKYTDVFQQQEIDLQTFLT-LTDQDLKELGITTFGARRKMLLAISELN 886
Cdd:cd09498     3 PDYPPNDLLEWLSLLGLPQYHKVLVENGYDSIDFVTdLTWEDLQDIGITKLGHQKKLMLAIKKLK 67

second type I K homology (KH) RNA-binding domain found in vigilin and similar proteins; Vigilin, also called high density lipoprotein-binding protein, or HDL-binding protein, is a ubiquitous and highly conserved RNA-binding protein that shuttles between nucleus and cytoplasm presumably in contact with RNA molecules. It may be involved in chromosome partitioning at mitosis, facilitating translation and tRNA transport, and control of mRNA metabolism, including estrogen-mediated stabilization of vitellogenin mRNA. Vigilin is up-regulated by cholesterol loading of cells and functions to protect cells from over-accumulation of cholesterol. It may play a role in cell sterol metabolism. Disruption of human vigilin impairs chromosome condensation and segregation. Vigilin has a unique structure of 14-15 consecutively arranged, but non-identical K-homology (KH) domains which apparently mediate RNA-protein binding. The model corresponds to the second one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628  78 LDTKSNrVTLKMDVSHteHSHVIGKGGNNIKKVMEETGCHIHFPdsnrnNQAEKSNQVSIAGQPAGVESARVRIR 152
Cdd:cd22406     1 LQTQAS-VTVNIPKEH--HRFILGKKGKKLQELELKTATKIVIP-----RQEDNSDEIKITGTKEGIEKARHEIQ 67

SAM domain of WDSUB1 proteins; SAM (sterile alpha motif) domain of WDSUB1 subfamily proteins is a putative protein-protein interaction domain. Proteins of this group contain multiple domains: SAM, one or more WD40 repeats and U-box (derived version of the RING-finger domain). Apparently the WDSUB1 subfamily proteins participate in protein degradation through ubiquitination, since U-box domain are known as a member of E3 ubiquitin ligase family, while SAM and WD40 domains most probably are responsible for an E2 ubiquitin-conjugating enzyme binding and a target protein binding.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1034569628 838 GLGKYTDVFQQQEIDLQTFLTLTDQDL-KELGITTFGARRKMLLAISEL 885
Cdd:cd09505    18 GLEQYVEVFRANNIDGKELLNLTKESLsKDLKIESLGHRNKILRKIEEL 66

first type I K homology (KH) RNA-binding domain found in the FUBP family RNA/DNA-binding proteins; The far upstream element-binding protein (FUBP) family includes FUBP1-3. FUBP1, also called FBP, or FUSE-binding protein 1, or DNA helicase V, or DH V, binds RNA and single-stranded DNA (ssDNA) and may act both as activator and repressor of transcription. It regulates MYC expression by binding to a single-stranded far-upstream element (FUSE) upstream of the MYC promoter. FUBP2, also called FUSE-binding protein 2, or KH type-splicing regulatory protein (KSRP), or p75, is a single-strand nucleic acid binding protein implicated in a variety of cellular processes, including splicing in the nucleus, mRNA decay, maturation of miRNA, and transcriptional control of proto-oncogenes such as c-myc. It regulates the stability and/or translatability of many mRNA species, encoding immune-relevant proteins, either by binding to AU-rich elements (AREs) of mRNA 3'UTR or by facilitating miRNA biogenesis to target mRNA. FUBP3, also called FUSE-binding protein 3, or MARTA2, was previously shown to mediate dendritic targeting of MAP2 mRNA in neurons. It may interact with single-stranded DNA from the far-upstream element (FUSE) and activate gene expression. It is required for beta-actin mRNA localization. It also interacts with fibroblast growth factor 9 (FGF9) 3'-UTR UG repeats and positively controls FGF9 expression through increasing translation of FGF9 mRNA. FUBP proteins contain four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1034569628  99 VIGKGGNNIKKVMEETGCHIHF-PDSnrNNQAEKSnqVSIAGQPAGVESARVRIRE 153
Cdd:cd22396    15 IIGRGGEQINRLQAESGAKIQIaPDS--GGLPERP--CTLTGTPDAIETAKRLIDQ 66

KH domain; KH motifs bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1034569628  22 GRSGEdFFQKIMEETNTQIawpsKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMS 76
Cdd:pfam00013  16 GKGGS-NIKEIREETGAKI----QIPPSESEGNERIVTITGTPEAVEAAKALIEE 65

type I K homology (KH) RNA-binding domain found in activating signal cointegrator 1 complex subunit 1 (ASCC1) and similar proteins; ASCC1, also called ASC-1 complex subunit p50, or Trip4 complex subunit p50, plays a role in DNA damage repair as component of the ASCC complex. It is part of the ASC-1 complex that enhances NF-kappa-B, SRF and AP1 transactivation. In cells responding to gastrin-activated paracrine signals, it is involved in the induction of SERPINB2 expression by gastrin. ASCC1 may also play a role in the development of neuromuscular junction.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1034569628  86 TLKMDVSHTEHSHVIGKGGNNIKKVMEETGCHIHFPDSNrnnqaeKSNQVSIAGQPA-GVESARVRIRELL 155
Cdd:cd22419     2 RLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQG------KEGDIVITGKDRsGVDSARTRIEVLV 66

SAM domain of USH1G; SAM (sterile alpha motif) domain of USH1G (Usher syndrome type-1G protein) proteins (also known as SANS) is a putative protein-protein interaction domain. Members of this group have an N-terminal ankyrin repeat region and C-terminal SAM domain. USH1G is expressed in the hair bundles of the inner ear sensory cells. It can form a functional network with USH1B (myosin VIIa), USH1C (harmonin b), USH1F (protocadherin-related 15), and USH1D (cadherin 23). The SAM domain of the USH1G protein is involved in synergetic interactions with the PDZ domain of harmonin. Such interactions contribute to the stability of harmonin. The network is required for the correct cohesion of the hair bundle. Mutations in the ush1g gene lead to Usher syndrome type 1G. This syndrome is the cause of deaf-blindness in humans.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1034569628 828 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGItTFGARRKMLLAIselnKNRRKLFESP 896
Cdd:cd09586     3 SPLEVFLASLSMEEFIAILKREKIDLDALLLCSDNDLKSIHI-PLGPRKKILDAC----QRRRQTIERP 66

second type I K homology (KH) RNA-binding domain found in the family of poly(C)-binding proteins (PCBPs); The PCBP family, also known as hnRNP E family, comprises four members, PCBP1-4, which are RNA-binding proteins that interact in a sequence-specific manner with single-stranded poly(C) sequences. They are mainly involved in various posttranscriptional regulations, including mRNA stabilization or translational activation/silencing. Besides, PCBPs may share iron chaperone activity. PCBPs contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.