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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078718  48 WSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSV 127
Cdd:cd22420     1 LVEERFRVDRRKLESMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSV 80

                  .
gi 1907078718 128 L 128
Cdd:cd22420    81 L 81

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 1907078718 286 PVSTQLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSN-PQKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd22422     1 PVSMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDPNNpPQRKSTVFISGSIDSVYLARQQLM 67

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078718  48 WSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSV 127
Cdd:cd22420     1 LVEERFRVDRRKLESMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSV 80

                  .
gi 1907078718 128 L 128
Cdd:cd22420    81 L 81

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 1907078718 286 PVSTQLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSN-PQKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd22422     1 PVSMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDPNNpPQRKSTVFISGSIDSVYLARQQLM 67

K homology RNA-binding domain;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078718  133 NRVTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNrnnqaEKSNQVSIAGQPAGVESARARIRELL 205
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPG-----SEERVVEITGPPENVEKAAELILEIL 68

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 1907078718 877 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 934
Cdd:pfam00536   6 EDVGEWLESIGLGQYIDSFRAGYIDGDALLQLTEDDLLKLGVTLLGHRKKILYAIQRL 63

Sterile alpha motif; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907078718  877 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQ-DLKELGITTFGARRKMLLAISEL 934
Cdd:smart00454   7 ESVADWLESIGLEQYADNFRKNGIDGALLLLLTSEeDLKELGITKLGHRKKILKAIQKL 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078718  50 EERFRVDRKKLEAMLqaaaegkGRSGEdFFQKIMEETNTQIawpsKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMS 126
Cdd:pfam00013   1 TVEILVPSSLVGLII-------GKGGS-NIKEIREETGAKI----QIPPSESEGNERIVTITGTPEAVEAAKALIEE 65

polynucleotide phosphorylase/polyadenylase; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078718 149 VIGKGGNNIKKVMEDTGCHIHFPDSNRnnqaeksnqVSIAG-QPAGVESARARIREL 204
Cdd:PRK11824  568 VIGPGGKTIREITEETGAKIDIEDDGT---------VKIAAtDGEAAEAAKERIEGI 615

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078718  48 WSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSV 127
Cdd:cd22420     1 LVEERFRVDRRKLESMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSV 80

                  .
gi 1907078718 128 L 128
Cdd:cd22420    81 L 81

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 1907078718 286 PVSTQLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSN-PQKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd22422     1 PVSMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDPNNpPQRKSTVFISGSIDSVYLARQQLM 67

SAM domain of ANKS3 subfamily; SAM (sterile alpha motif) domain of ANKS3 subfamily is a potential protein-protein interaction domain. Proteins of this subfamily have N-terminal ankyrin repeats and a C-terminal SAM domain. SAM is a widespread domain in signaling proteins. In many cases it mediates homo-dimerization/oligomerization.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907078718 877 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 934
Cdd:cd09519     5 KDLSELLEQIGCSKYLPIFEEQDIDLRIFLTLTESDLKEIGITLFGPKRKMTSAIARW 62

first type I K homology (KH) RNA-binding domain found in Caenorhabditis elegans defective in germ line development protein 3 (CeGLD-3) and similar proteins; CeGLD-3, also called germline development defective 3, is a Bicaudal-C (Bic-C) homolog that is involved in the translational control of germline-specific mRNAs during embryogenesis. It interacts with the cytoplasmic poly(A)-polymerase GLD-2. The two proteins cooperate to recognize target mRNAs and convert them into a polyadenylated, translationally active state. CeGLD-3 contains four K-homology (KH) RNA-binding domains, which are divergent KH domains that lacks the RNA-binding GXXG motif. The model corresponds to the first one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907078718 134 RVTLKMDVSHTEHSHVIGK--GGNNIKKVMEDTGCHIHFPDSNRNNQAEKSNQVSIAGQPAGVESARARIR 202
Cdd:cd22441     1 RVTLNMEFESQYHSLMTSDngDHENIASIMAETSTLIQFPDRSVGGPEPFANQVTITGYFVNVERARMRMR 71

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 1907078718 136 TLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNnqaEKSNQVSIAGQPAGVESARARIRE 203
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESE---GNERIVTITGTPEAVEAAKALIEE 65

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 1907078718 878 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISELS 935
Cdd:cd09518     7 ELSGILRKLSLEKYQPIFEEQEVDMEAFLTLTDGDLKELGIKTDGPRQQILAAISELN 64

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 1907078718 137 LKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQaekSNQVSIAGQPAGVESARARIR 202
Cdd:cd00105     1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSG---ERVVTITGTPEAVEKAKELIE 63

Sterile alpha motif; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerisation.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907078718  877 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQ-DLKELGITTFGARRKMLLAISEL 934
Cdd:smart00454   7 ESVADWLESIGLEQYADNFRKNGIDGALLLLLTSEeDLKELGITKLGHRKKILKAIQKL 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 1907078718 133 NRVTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRnnqaEKSNQVSIAGQPAGVESARARI 201
Cdd:cd22413     1 NSFTVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARD----EDQELITIIGTKEAVEKAKEEL 65

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 1907078718 290 QLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSNPQKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd00105     2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELIE 63

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 1907078718 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQaeksNQVSIAGQPAGVESARARIRELL 205
Cdd:cd22417     1 FTLTVEVDPKYHPKIIGRKGAVITKLRDDHDVNIQFPDKGDEND----DEITITGYEKNAEAAKDAILKIV 67

eighth 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 eighth one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907078718 146 HSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNnqaekSNQVSIAGQPAGVESARARI 201
Cdd:cd22411    11 HKNIIGKGGATIKKIREETNTRIDLPEENSD-----SDVITITGKKEDVEKARERI 61

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 1907078718 288 STQLDIAA--QHHLFMMGRNGSNVKHIMQRTGAQIHFPdPSNPQKKSTVYLQGTIESVCLARQYL 350
Cdd:cd22413     2 SFTVEIRAkpEYHRFLIGRGGANIRKIRDNTGARIIFP-TARDEDQELITIIGTKEAVEKAKEEL 65

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1907078718 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNqaekSNQVSIAGQPAGVESARARIREL 204
Cdd:cd22418     1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDAD----PNLVTITGLEENVEECKDHLLNL 66

thirteenth 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 thirteenth one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907078718 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNrnnqaEKSNQVSIAGQPAGVESARA----RIREL 204
Cdd:cd22416     2 VTEEVNVPFDLHRFIIGQKGADVRKMMDEFDVNISIPPAE-----LQSDIIKITGPPANVERAKAalleRVKEL 70

SAM domain of ASZ1 subfamily; SAM (sterile alpha motif) domain of ASZ1 (Ankyrin, SAM, leucine Zipper) also known as GASZ (Germ cell-specific Ankyrin, SAM, leucine Zipper) subfamily is a potential protein-protein interaction domain. Proteins of this group are involved in the repression of transposable elements during spermatogenesis, oogenesis, and preimplantation embryogenesis. They support synthesis of PIWI-interacting RNA via association with some PIWI proteins, such as MILI and MIWI. This association is required for initiation and maintenance of retrotransposon repression during the meiosis. In mice lacking ASZ1, DNA damage and delayed germ cell maturation was observed due to retrotransposons releasing from their repressed state.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078718 872 SCFKGSDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 934
Cdd:cd09521     1 SYSKLDDLELFLHGLELGHLTPLFKEHDVTFSQLLKMTEEDLEKIGITQPGDQKKILDAIKEV 63

fourth 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 fourth one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1907078718 136 TLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFpdsnrnNQAEKSNQVSIAGQPAGVESARARIREL 204
Cdd:cd22449     5 TVKFDVPAKYVPHIIGKKGANINKLREEYGVKIDF------EDKTGEGNVEIKGSKKNVEEAKKRILSQ 67

SAM domain of DDHD2; SAM (sterile alpha motif) domain of DDHD2 group is a potential protein-protein interaction domain. DDHD2 proteins contain at least two domains:a SAM domain and a predicted metal-binding domain. Phospholipase A1 activity was demonstrated for the mammalian DDHD2 protein. Mutation of the putative catalytic serine resulted in elimination of activity. Unlike SEC23IP, DDHD2 proteins do not have an N-terminal proline-rich region and correspondingly they are not able to interact with Sec23p/Sec24p complex. Overexpression of DDHD2 is the cause of dispersion of ER/Golgi intermediate compartment and dispersion of tethering proteins located in the Golgi region, leading to aggregation in the endoplasmic reticulum.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1907078718 879 LPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGItTFGARRKMLLAIS 932
Cdd:cd09585    12 LEETLKKLGLSEYCDVFEKEKIDLEALALCQERDLKDLGI-PLGPRKKILNYIR 64

SAM domain of TAL subfamily; SAM (sterile alpha motif) domain of TAL (Tsg101-associated ligase) proteins, also known as LRSAM1 (Leucine-rich repeat and sterile alpha motif-containing) proteins, is a putative protein-protein interaction domain. Proteins of this subfamily participate in the regulation of retrovirus budding and receptor endocytosis. They show E3 ubiquitin ligase activity. Human TAL protein interacts with Tsg101 and TAL's C-terminal ring finger domain is essential for the multiple monoubiquitylation of Tsg101.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078718 878 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 934
Cdd:cd09523     7 QLVNLLNELSAEHYLPVFARHRITMETLSTMTDEDLKKIGIHEIGLRKEILRAAQEL 63

ninth 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 ninth one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907078718 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDT-GCHIHFPDSNrnnqaEKSNQVSIAGQPAGVESARARIREL 204
Cdd:cd22412     2 VEVEVEIPAKLHNSLIGAKGRLIRSIMEECgGVHIHFPPEG-----SGSDKVTIRGPKEDVEKAKKQLLEL 67

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 1907078718 136 TLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNnqaekSNQVSIAGQPAGVESARARI 201
Cdd:cd22408     1 TVSVEVPKSQHRFVIGPRGSTIQEILEETGCSVEVPPNDSD-----SETITLRGPADKLGAALTLV 61

seventh 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 seventh one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907078718 140 DVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQAeksnqVSIAGQPAGVESARARIRE 203
Cdd:cd22452     7 KVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDV-----ITLRGTKEGVEKAEEMIKK 65

SAM domain of sec23ip; SAM (sterile alpha motif) domain of Sec23ip (Sec23 interacting protein) group is a potential protein-protein interaction domain. Sec23ip proteins (also known as p125) contain an N-terminal proline-rich region, a central region containing a SAM domain and a C-terminal region with a predicted metal-binding domain. Sec23ip interacts with Sec23p/Sec24p part of COPII-coated vesicles complex involved in protein transport from the ER to the Golgi apparatus. The proline-rich region plays an essential role in this interaction. Overexpression of Sec23ip leads to disorganization of ER/Golgi intermediate compartment.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1907078718 878 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGItTFGARRKmllaISELSKNRRK 940
Cdd:cd09584    11 SLQSVLEALSLSEYKSTFEKEKIDMESLLMCTVDDLKEMGI-PLGPRKK----IANFVKEKAA 68

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 1907078718 884 SKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 934
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 1907078718 149 VIGKGGNNIKKVMEDTGCH-IHFPDSNRNNQAEKSnqVSIAGQPAGVESARARIRELL 205
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 1907078718 878 DLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAISEL 934
Cdd:cd09524     7 SISQFLSSLGLEHLREIFEREQITLDVLAEMGHEELKEIGINAYGHRHKLIKGVERL 63

fifth 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 fifth one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907078718 146 HSHVIGKGGNNIKKVMEDT-GCHIHFPdsnrnnqaEKSNQVSIAGQPAGVESARARIRE 203
Cdd:cd22409    13 HRFIIGKKGANIKKITQDLpKVHIEFT--------EGEDKIELEGPPEEVEVVREQLEA 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 1907078718 879 LPELFSKLGLGKYTDVFQQqeIDLQTFLTLTDQDLKELGITTFGARRKMLLAI 931
Cdd:cd09489     2 IPMWLKSLRLHKYSDAFKG--TTWEELLYLTEETLEKKGVLTLGARRKLLKAF 52

eighth 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 eighth one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907078718  72 GRSGEDFfQKIMEETNTQIAWPSKlkigaKSKKDPhIKVSGKKEDVKEAKEMI 124
Cdd:cd22411    16 GKGGATI-KKIREETNTRIDLPEE-----NSDSDV-ITITGKKEDVEKARERI 61

sixth 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 sixth one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078718 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPdsnrnNQAEKSNQVSIAGQPAGVESARARI 201
Cdd:cd22451     1 ASIDIDIPKEYHRAIIGKGGAVLRELEAETGCRIQVP-----KKDDPSGKIRITGARDGVEAATAKI 62

SAM domain of Smaug subfamily; SAM (sterile alpha motif) domain of Smaug proteins is an RNA recognition domain. It binds a specific RNA motif known as Smaug recognition element (SRE). Among members of this group are invertebrate Smaug (Smg) proteins and vertebrate Smaug1 and Smaug2 proteins. They are involved in post-transcriptional control during early embryogenesis in animals. In Drosophila, Smaug protein is a translational repressor of mRNA of Nanos (Nos) protein. Gradient of Nanos is required for proper abdominal segmentation. SAM domain interacts specifically with the Nanos mRNA regulatory regions. Moreover, Smaug protein is involved in regulation of specific maternal transcripts degradation in Drosophila early embryo via recruitment of the CCR4/POP2/NOT deadenylase.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1907078718 877 SDLPELFSKLGLGKYTDVFQQqeIDLQTFLTLTDQDLKELGITTfGARRKMLLAISEL 934
Cdd:cd09557     7 KDVPAWLKSLRLHKYASLFSQ--MTYEEMLNLTEEQLEAQGVTK-GARHKIALSIQKL 61

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 1907078718 128 LDTKSNrVTLKMDVSHteHSHVIGKGGNNIKKVMEDTGCHIHFPdsnrnNQAEKSNQVSIAGQPAGVESARARIR 202
Cdd:cd22406     1 LQTQAS-VTVNIPKEH--HRFILGKKGKKLQELELKTATKIVIP-----RQEDNSDEIKITGTKEGIEKARHEIQ 67

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 1907078718 149 VIGKGGNNIKKVMEDTGCHIHF-PDSnrNNQAEKSnqVSIAGQPAGVESARARIRE 203
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        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1907078718  50 EERFRVDRKKLEAMLqaaaegkGRSGEdFFQKIMEETNTQIawpsKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMS 126
Cdd:pfam00013   1 TVEILVPSSLVGLII-------GKGGS-NIKEIREETGAKI----QIPPSESEGNERIVTITGTPEAVEAAKALIEE 65