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 1103360258  48 WSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSV 127
Cdd:cd22420     1 LVEERFRVDRRKLESMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSV 80

                  .
gi 1103360258 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 1103360258 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 1103360258  48 WSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSV 127
Cdd:cd22420     1 LVEERFRVDRRKLESMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSV 80

                  .
gi 1103360258 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 1103360258 286 PVSTQLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSN-PQKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd22422     1 PVSMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDPNNpPQRKSTVFISGSIDSVYLARQQLM 67

K homology RNA-binding domain;

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1103360258  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 1103360258 878 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAI 932
Cdd:pfam00536   6 EDVGEWLESIGLGQYIDSFRAGYIDGDALLQLTEDDLLKLGVTLLGHRKKILYAI 60

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 1103360258  878 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQ-DLKELGITTFGARRKMLLAISV 934
Cdd:smart00454   7 ESVADWLESIGLEQYADNFRKNGIDGALLLLLTSEeDLKELGITKLGHRKKILKAIQK 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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1103360258  50 EERFRVDRKKLEAMLqaaaegkGRSGEdFFQKIMEETNTQIawpsKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMS 126
Cdd:pfam00013   1 TVEILVPSSLVGLII-------GKGGS-NIKEIREETGAKI----QIPPSESEGNERIVTITGTPEAVEAAKALIEE 65

polynucleotide phosphorylase/polyadenylase; Provisional

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1103360258 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 1103360258  48 WSEERFRVDRKKLEAMLQAAAEGKGRSGEDFFQKIMEETNTQIAWPSKLKIGAKSKKDPHIKVSGKKEDVKEAKEMIMSV 127
Cdd:cd22420     1 LVEERFRVDRRKLESMLQAAAEGKGENGEDFFQKIMEETNTQITWPSKLKIGAKSKKDPHVKVAGKPENVQEAKEKILSV 80

                  .
gi 1103360258 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 1103360258 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 1103360258 878 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAIS 933
Cdd:cd09519     5 KDLSELLEQIGCSKYLPIFEEQDIDLRIFLTLTESDLKEIGITLFGPKRKMTSAIA 60

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 1103360258 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 1103360258 136 TLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNnqaEKSNQVSIAGQPAGVESARARIRE 203
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 1103360258 878 SDLPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAI 932
Cdd:pfam00536   6 EDVGEWLESIGLGQYIDSFRAGYIDGDALLQLTEDDLLKLGVTLLGHRKKILYAI 60

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 1103360258 137 LKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQaekSNQVSIAGQPAGVESARARIR 202
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 1103360258 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSnrNNQAEKSNQVSIAGQPAGVESARARI 201
Cdd:cd22422     2 VSMQLEIAPQHHLFMLGRNGSNIKHIMQRTGAQIHFPDP--NNPPQRKSTVFISGSIDSVYLARQQL 66

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 1103360258 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 1103360258 290 QLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSNPQKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd00105     2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELIE 63

second 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 second one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1103360258 132 SNRVTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPdsNRNNQAEKSN-------QVSIAGQPAGVESARARIRE 203
Cdd:cd22447     1 SPKQNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIP--PRDADAAPADedddtmvEVTITGDEFNVQHAKQRIEE 77

SAM domain (Sterile alpha motif);

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1103360258 878 SDLPELFSKLGLGKYTDVFQQQEID-LQTFLTLTDQDLKELGITTFGARRKMLLAI 932
Cdd:pfam07647   7 ESVADWLRSIGLEQYTDNFRDQGITgAELLLRLTLEDLKRLGITSVGHRRKILKKI 62

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 1103360258 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 1103360258 135 VTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNqaekSNQVSIAGQPAGVESARARIREL 204
Cdd:cd22418     1 VTEEVEIDSRVHPRLIGARGKAIRKIMEDFKVDIRFPRSGDAD----PNLVTITGLEENVEECKDHLLNL 66

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 1103360258 287 VSTQLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDP--SNPQKKST-VYLQGTIESVCLARQ 348
Cdd:cd22421     3 VTLKMDVSHTDHSHVIGKGGNNIKKVMEDTGCHIHFPDSnrTSQAEKSNqVSIAGQPAGVESARA 67

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 1103360258 291 LDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSNpqKKSTVYLQGTIESVCLARQYLM 351
Cdd:cd22407     4 LDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSV--NKDEIVVSGEKEGVAQAVAKIK 62

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 1103360258 880 LPELFSKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGItTFGARRKMLLAIS 933
Cdd:cd09585    12 LEETLKKLGLSEYCDVFEKEKIDLEALALCQERDLKDLGI-PLGPRKKILNYIR 64

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 1103360258 149 VIGKGGNNIKKVMEDTGCHIHF--PDSNRNNQaeksnQVSIAGQPAGVESARARIREL 204
Cdd:cd22454    18 VIGKGGETIKRIEALTDTVITFerVNGGSPNR-----EVQITGSPDNVAAAKRLIEDT 70

SAM domain of VTS1 RNA-binding proteins; SAM (sterile alpha motif) domain of VTS1 subfamily proteins is RNA binding domain located in the C-terminal region. SAM interacts with stem-loop structures of mRNA. Proteins of this subfamily participate in regulation of transcript stability and degradation, and also may be involved in vacuolar protein transport regulation. VTS1 protein of S.cerevisiae induces mRNA degradation via the major deadenylation-dependent mRNA decay pathway; VTS1 recruits CCR4/POP2/NOT deadenylase complex to target mRNA. The recruitment is the initial step resulting in poly(A) tail removal transcripts. Potentially SAM domain may be responsible not only for RNA binding but also for deadenylase binding.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1103360258 879 DLPELFSKLGLGKYTDVFQqqEIDLQTFLTLTDQDLKELGITTFGARRKML 929
Cdd:cd09556     8 DIPAWLRSLRLHKYTDNLK--DLSWKELIELDDEDLEDKGVSALGARRKLL 56

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 1103360258 138 KMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNqaeksNQVSIAGQPAGVESARARIR 202
Cdd:cd22407     3 RLDIPKVYHPFIAGPNNENVKELQEETGVRINIPPPSVNK-----DEIVVSGEKEGVAQAVAKIK 62

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 1103360258 140 DVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNRNNQAeksnqVSIAGQPAGVESARARIRE 203
Cdd:cd22452     7 KVSPRYFGRIIGPGGSNINQIREKSGCFINVPKKNKESDV-----ITLRGTKEGVEKAEEMIKK 65

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 1103360258 149 VIGKGGNNIKKVMEDTGCHIHF-PDsnRNNQAEKSNQVSiaGQPAGVESARARIRELL 205
Cdd:cd22398    14 VIGKGGEMIKKIQNETGARVQFkPD--DGNSPDRICVIT--GPPDQVQHAARMIQELI 67

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 1103360258 286 PVSTQLDIAAQHHLFMMGRNGSNVKHIMQRTGAQIHFPDPSNPQkkSTVYLQGTIESVCLARQ 348
Cdd:cd02394     1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANS--DEIRIEGSPEGVKKAKA 61

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 1103360258 149 VIGKGGNNIKKVMEDTGCH-IHFPDSNRNNQAEKSnqVSIAGQPAGVESARARIRELL 205
Cdd:cd22397    14 IIGKGGETIKQLQERAGVKmVMIQDGPQPTGQDKP--LRITGDPQKVQRAKELVMELI 69

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 1103360258 146 HSHVIGKGGNNIKKVMEDT-GCHIHFPdsnrnnqaEKSNQVSIAGQPAGVESARARIRE 203
Cdd:cd22409    13 HRFIIGKKGANIKKITQDLpKVHIEFT--------EGEDKIELEGPPEEVEVVREQLEA 63

fifth 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 fifth one.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1103360258 132 SNRVTLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCH---------IHFPdsnrnNQAEKSNQVSIAGQPAGVESARARIR 202
Cdd:cd22450     1 EDEVTRTIKVDRKYHRTIIGPGGSTLRELISKAGGPtdrqeqarlVRFP-----NQNSESDEVVIRGPKKIVEKIIAEIE 75

                  ..
gi 1103360258 203 EL 204
Cdd:cd22450    76 KI 77

SAM domain of BOI-like fungal subfamily; SAM (sterile alpha motif) domain of BOI-like fungal subfamily is a potential protein-protein interaction domain. Proteins of this subfamily are apparently scaffold proteins, since most contain SH3 and PH domains, which are also protein-protein interaction domains, in addition to SAM domain. BOI-like proteins participate in cell cycle regulation. In particular BOI1 and BOI2 proteins of budding yeast S.cerevisiae are involved in bud formation, and POB1 protein of fission yeast S.pombe plays a role in cell elongation and separation. Among binding partners of BOI-like fungal subfamily members are such proteins as Bem1 and Cdc42 (they are known to be involved in cell polarization and bud formation).

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1103360258 893 TDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAI 932
Cdd:cd09535    22 CEKFRENEITGDILLELDLEDLKELDIGSFGKRFKLWNEI 61

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 1103360258  72 GRSGEDFfQKIMEETNTQIAWPSKlkigaKSKKDPhIKVSGKKEDVKEAKEMI 124
Cdd:cd22411    16 GKGGATI-KKIREETNTRIDLPEE-----NSDSDV-ITITGKKEDVEKARERI 61

SAM domain of diacylglycerol kinase delta and eta subunits; SAM (sterile alpha motif) domain of DGK-eta-delta subfamily proteins is a protein-protein interaction domain. Proteins of this subfamily are multidomain diacylglycerol kinases with a SAM domain located at the C-terminus. DGK proteins participate in signal transduction. They regulate the level of second messengers such as diacylglycerol and phosphatidic acid. The SAM domain of DGK proteins can form high molecular weight homooligomers through head-to-tail interactions as well as heterooligomers between the SAM domains of DGK delta and eta proteins. The oligomerization plays a role in the regulation of DGK intracellular localization.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1103360258 885 SKLGLGKYTDVFQQQEIDLQTFLTLTDQDLKELGITTFGARRKMLLAI 932
Cdd:cd09507    15 ESLQLGEYRDIFARNDIRGSELLHLERRDLKDLGITKVGHVKRILQAI 62

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 1103360258 149 VIGKGGNNIKKVMEDTGCHIHFpdsNRNNQAEKSNQV-SIAGQPAGVESARARIRE 203
Cdd:cd22399    14 VIGKGGETIRQINQQSGAHVEL---DRNPPPNPNEKLfIIRGNPQQIEHAKQLIRE 66

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 1103360258 128 LDTKSNrVTLKMDVSHteHSHVIGKGGNNIKKVMEDTGCHIHFPdsnrnNQAEKSNQVSIAGQPAGVESARARIR 202
Cdd:cd22406     1 LQTQAS-VTVNIPKEH--HRFILGKKGKKLQELELKTATKIVIP-----RQEDNSDEIKITGTKEGIEKARHEIQ 67

type I K homology (KH) RNA-binding domain found in Mask family proteins; The Mask family includes Drosophila melanogaster ankyrin repeat and KH domain-containing protein Mask, and its mammalian homologues Mask1/ANKHD1 and Mask2/ANKRD17. Mask, also called multiple ankyrin repeat single KH domain-containing protein, is a large ankyrin repeat and KH domain-containing protein involved in Drosophila receptor tyrosine kinase signaling. It acts as a mediator of receptor tyrosine kinase (RTK) signaling and may act either downstream of MAPK or transduce signaling through a parallel branch of the RTK pathway. Mask is required for the development and organization of indirect flight muscle sarcomeres by regulating the formation of M line and H zone and the correct assembly of thick and thin filaments in the sarcomere. Mask1/ANKHD1, also called HIV-1 Vpr-binding ankyrin repeat protein, or multiple ankyrin repeats single KH domain, or Hmask, is highly expressed in various cancer tissues and is involved in cancer progression, including proliferation and invasion. Mask2/ANKRD17, also called ankyrin repeat protein 17, or gene trap ankyrin repeat protein (GTAR), or serologically defined breast cancer antigen NY-BR-16, is a ubiquitously expressed ankyrin factor essential for the vascular integrity during embryogenesis. It may be directly involved in the DNA replication process and play pivotal roles in cell cycle and DNA regulation. It is also involved in innate immune defense against bacteria and viruses.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1103360258 138 KMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFpdsNRNNQAEKSNQVSIAGQPAGVESARARIRELL 205
Cdd:cd22404     4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEI---DKQKGEQGDRRITIKGSADATRQAAQLINALI 68

second type I K homology (KH) RNA-binding domain found in the insulin-like growth factor 2 mRNA-binding protein (IGF2BP) family; The IGF2BP family includes three members: IGF2BP1/IMP-1/ CRD-BP/ VICKZ1, IGF2BP2/IMP-2/ VICKZ2, and IGF2BP3/IMP-3/VICKZ3, which are RNA-binding factors that recruit target transcripts to cytoplasmic protein-RNA complexes (mRNPs). They function by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. IGF2BP proteins contain four K-homology (KH) RNA-binding domains which are important in RNA binding and are known to be involved in RNA synthesis and metabolism. The model corresponds to the second one.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1103360258 301 MMGRNGSNVKHIMQRTGAQI-----HFPDPSNPQKKSTVYlqGTIESVCLARQYLM 351
Cdd:cd22401    14 LIGKDGRNIKKIMEDTNTKItisslQDLTSYNPERTITIK--GSLEAMSEAESLIS 67

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 1103360258 878 SDLPELFSKLGLGKYTDVFQQqeIDLQTFLTLTDQDLKELGITTfGARRKMLLAI 932
Cdd:cd09557     7 KDVPAWLKSLRLHKYASLFSQ--MTYEEMLNLTEEQLEAQGVTK-GARHKIALSI 58

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 1103360258 136 TLKMDVSHTEHSHVIGKGGNNIKKVMEDTGCHIHFPDSNrnnqaeKSNQVSIAGQPA-GVESARARIRELL 205
Cdd:cd22419     2 RLSLDVPSALFKFIIGKKGETKKRLESETKTQIRIPRQG------KEGDIVITGKDRsGVDSARTRIEVLV 66