Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 328 SRSLQLDKLVNEMTQHYENSVPED--LTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20412     1 SRSLQLDKLVQEMTQYYESEENRHtlLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                          90
                  ....*....|....*
gi 2217263382 406 RSDFLSLPFQAIECS 420
Cdd:cd20412    81 RSDFLSLPFQAIECS 95

first type I K homology (KH) RNA-binding domain found in tudor and KH domain-containing protein (TDRKH) and similar proteins; TDRKH, also called tudor domain-containing protein 2 (TDRD2), is a mitochondria-anchored RNA-binding protein that is required for spermatogenesis and involved in piRNA biogenesis. It specifically recruits MIWI, but not MILI, to engage the piRNA pathway. TDRKH contains two K-homology (KH) RNA-binding domains and one tudor domain, which are involved in binding to RNA or single-strand DNA. The model corresponds to the first one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2217263382  49 GEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD---ERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22428     1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGelpERVLLIQGNPVQAQRAEEAIHQII 74

Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 328 SRSLQLDKLVNEMTQHYENSVPED--LTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20412     1 SRSLQLDKLVQEMTQYYESEENRHtlLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                          90
                  ....*....|....*
gi 2217263382 406 RSDFLSLPFQAIECS 420
Cdd:cd20412    81 RSDFLSLPFQAIECS 95

Tudor domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 306 EYLEVYVSASEHPNHFWIQIVgSRSLQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLD 385
Cdd:pfam00567   1 STIDVVVSHIESPSTFYIQPK-SDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSEDGKWYRAKITESLDDGLVE 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2217263382 386 LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:pfam00567  80 VLFIDYGNTETVPLSDLRPLPPELESLPPQAIKCQLA 116

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 2217263382  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIpPSESEGNERIVTITGTPEAVEAAKALIEE 65

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2217263382   51 DDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-EERVVEITGPPENVEKAAELILEIL 68

rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDvGDerVLLISGF-PVQVCKAKAAIHQI---------------- 118
Cdd:COG1094     3 YVKIPKDRIGVLIGKGGETKKEIEEKTGVKLDIDSET-GE--VTIEPGEdPLAALKARDIVKAIgrgfspekalrllddd 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2217263382 119 -------LTENTPVSEQLsvpQRSVGRIIGRGGETIRSICKASGAKI 158
Cdd:COG1094    80 ymlevidLPDVGKSPNAL---DRIKGRIIGREGRTRRIIEELTGVDI 123

arCOG04150 universal archaeal KH domain protein; This family of proteins is universal among the 41 archaeal genomes analyzed, and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDvGDERVLLISGFPVQVCKAKAAIHQI----------------- 118
Cdd:TIGR03665   1 YVKIPKDRIGVLIGKGGETKKEIEERTGVKLDIDSET-GEVKIEPEDEDPLAVMKAREVVKAIgrgfspekalklldddy 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 2217263382 119 ------LTENTPVSEQLsvpQRSVGRIIGRGGETIRSICKASGAKI 158
Cdd:TIGR03665  80 mlevidLKEYGKSPNAL---RRIKGRIIGEGGKTRRIIEELTGVSI 122

Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*
gi 2217263382  355 HVGDIVAAPLpTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDF 409
Cdd:smart00333   4 KVGDKVAARW-EDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57

Tudor domain found in Tudor domain-containing protein 2 (TDRD2) and similar proteins; TDRD2, also called Tudor and KH domain-containing protein (TDRKH), participates in the primary piwi-interacting RNA (piRNA) biogenesis pathway and is required during spermatogenesis to repress transposable elements and prevent their mobilization, which is essential for germline integrity. The family also includes the TDRD2 homolog found in Drosophila melanogaster (dTDRKH), which is also called partner of PIWIs protein, or PAPI, and is involved in Zucchini-mediated piRNA 3'-end maturation. TDRD2 contains two KH domains and one Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 328 SRSLQLDKLVNEMTQHYENSVPED--LTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20412     1 SRSLQLDKLVQEMTQYYESEENRHtlLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                          90
                  ....*....|....*
gi 2217263382 406 RSDFLSLPFQAIECS 420
Cdd:cd20412    81 RSDFLSLPFQAIECS 95

Tudor domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 306 EYLEVYVSASEHPNHFWIQIVgSRSLQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLD 385
Cdd:pfam00567   1 STIDVVVSHIESPSTFYIQPK-SDSKKLEKLTEELQEYYASKPPESLPPAVGDGCVAAFSEDGKWYRAKITESLDDGLVE 79

                          90       100       110
                  ....*....|....*....|....*....|....*..
gi 2217263382 386 LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:pfam00567  80 VLFIDYGNTETVPLSDLRPLPPELESLPPQAIKCQLA 116

Tudor domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope, where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. It contains a C-terminal Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2217263382 354 VHVGDIVAAPlpTNGSWYRARVLGTLENGNL-DLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20407     5 IEVGVICAAP--VMNAWYRAQVVGVFEETDEvEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

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 2217263382  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQVCKAKAAIHQ 117
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIpPSESEGNERIVTITGTPEAVEAAKALIEE 65

first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; TDRD1, also called cancer/testis antigen 41.1 (CT41.1), plays a central role during spermatogenesis by participating in the repression transposable elements and preventing their mobilization, which is essential for germline integrity. It acts via the piRNA metabolic process, which mediates the repression of transposable elements during meiosis by forming complexes composed of piRNAs and Piwi proteins, and governs the methylation and subsequent repression of transposons. TDRD1 contains four Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 310 VYVSASEHPNHFWIQIVGSRSLQ-LDKLVNEMTQHYENSVPEDLTV-HVGDIVAAPLPTNGSWYRARVlgtlENGNLD-- 385
Cdd:cd20408     1 GTVTEFKNPGEFYIQIYTLEVLEsLVKLTSQLKKTYASVNNHKEYIpEVGEVCVAKYSEDQNWYRALV----QTVDVQqk 76

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2217263382 386 ---LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGDQWEEEAL 436
Cdd:cd20408    77 kagVFYIDYGNEETVPLNRIQPLKKDIELFPPCAIKCCLANVKPPSGSWSEECI 130

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 2217263382 127 EQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLIL 191
Cdd:cd00105     1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGS--GERVVTITGTPEAVEKAKELIE 63

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2217263382 125 VSEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlLLSRLIKISGTQKEVAAAKHLI 190
Cdd:cd22396     1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGG--LPERPCTLTGTPDAIETAKRLI 64

second Tudor domain found in Tudor domain-containing protein 4 (TDRD4) and similar proteins; TDRD4, also called RING finger protein 17 (RNF17), is a component of the mammalian germ cell nuage and is essential for spermiogenesis. It seems to be involved in the regulation of transcriptional activity of MYC. In vitro, TDRD4 inhibits the DNA-binding activity of Mad-MAX heterodimers. It can recruit Mad transcriptional repressors (MXD1, MXD3, MXD4 and MXI1) to the cytoplasm. TDRD4 also acts as a potential cancer/testis antigen in liver cancer. TDRD4 contains a RING finger and five Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 367 NGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 426
Cdd:cd20415    37 DGAWYRARIIGLPGHREVEVKYVDFGNTATVTIKHVRKIKDDFLSLPEKARECRLAFIEP 96

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2217263382  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQVCKAKAAIHQI 118
Cdd:cd22396     1 VTEEYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGlPERPCTLTGTPDAIETAKRLIDQI 67

Tudor domain found in Drosophila melanogaster maternal protein Tudor (dTUD) and similar proteins; dTUD is required during oogenesis for the formation of primordial germ cells and for normal abdominal segmentation. It contains 11 Tudor domains. The family also includes mitochondrial A-kinase anchor protein 1 (AKAP1) and Tudor domain-containing proteins (TDRDs). AKAP1, also called A-kinase anchor protein 149 kDa (AKAP 149), or dual specificity A-kinase-anchoring protein 1 (D-AKAP-1), or protein kinase A-anchoring protein 1 (PRKA1), or Spermatid A-kinase anchor protein 84 (S-AKAP84), is found in mitochondria and in the endoplasmic reticulum-nuclear envelope where it anchors protein kinases, phosphatases, and a phosphodiesterase. It regulates multiple cellular processes governing mitochondrial homeostasis and cell viability. AKAP1 binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane. TDRDs have diverse biological functions and may contain one or more copies of the Tudor domain. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2217263382 356 VGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 405
Cdd:cd20379     1 VGDLCAAKYEEDGKWYRARVLEVLSNDKVEVFFVDYGNTETVPLSDLRPL 50

third Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 307 YLEVYVSASEHPNHFWIQIvGSRSLQLDKLVNEMTQHYENSVPED---LTVHVGDIVAAPLPTNGsWYRARVLGTLENGn 383
Cdd:cd20422     1 FYDAQVEFVKDPSEFWIRL-GEHAVPFSKLMRSMTAFYSQASKLDgvvLKPQPGQLCCAKWKEDR-YYRAIVTAVKGKM- 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2217263382 384 LDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGDQWEEEALDEFDR 441
Cdd:cd20422    78 VEVFLVDRGNTEMVDWYDVKKLLPQFRELPALALKCCLADICPLGERWSPEAISAFKR 135

third type I K homology (KH) RNA-binding domain found in heterogeneous nuclear ribonucleoprotein K (hnRNP K) and similar proteins; hnRNP K, also called transformation up-regulated nuclear protein (TUNP), is a pre-mRNA binding protein that binds tenaciously to poly(C) sequences. It may be involved in the nuclear metabolism of hnRNAs, particularly for pre-mRNAs that contain cytidine-rich sequences. It can also bind poly(C) single-stranded DNA. hnRNP K plays an important role in p53/TP53 response to DNA damage, acting at the level of both transcription activation and repression. hnRNP K contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2217263382 124 PVSEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTllLSRLIKISGTQKEVAAAKHLILEKVSE 196
Cdd:cd22434     1 TTTTQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGS--EDRIITITGTQDQIQNAQYLLQNSVKQ 71

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2217263382 126 SEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEgTLLLSRLIKISGTQKEVAAAKHLILEK 193
Cdd:cd22399     1 EVTFLVPANKCGLVIGKGGETIRQINQQSGAHVELDRNPP-PNPNEKLFIIRGNPQQIEHAKQLIREK 67

fourth Tudor domain found in Tudor domain-containing protein 6 (TDRD6) and similar proteins; TDRD6, also called antigen NY-CO-45 or cancer/testis antigen 41.2 (CT41.2), is a testis-specific expressed protein that was localized to the chromatoid bodies in germ cells, and is involved in spermiogenesis, chromatoid body formation, and for proper precursor and mature miRNA expression. Mutations in TDRD6 may be associated with human male infertility and early embryonic lethality. TDRD6 contains seven Tudor domains. This model corresponds to the fourth one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2217263382 367 NGSWYRARVLGTLEN-GNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLAR-IAPSG 428
Cdd:cd20423    16 DGKWCRALIDNVYEPvEMVEVTYVDYGNKELVSLKNLRSISEEFLKLKAQAFRCSLYNlIQPSG 79

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        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217263382 124 PVSEQLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGtlllSRLIKISGTQKEVAAAKHLILEKVS 195
Cdd:cd02394     1 MAFTTIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEAN----SDEIRIEGSPEGVKKAKAEILELVD 68

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 2217263382  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVLLISGFPVQVCKAKAAIH 116
Cdd:cd22413     4 TVEIRAKPEYHRFLIGRGGANIRKIRDNTGARIIFPTARDEDQELITIIGTKEAVEKAKEELE 66

first Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 334 DKLVNEMTQHYENSV--PEDLTVHVGDIVAAPlPTNGSWYRARVLGTLENgNLDLYFVDFGDNGDCPLKDLRALRSDFLS 411
Cdd:cd20427     1 EQMEDEMKEFYSKSStaMCLRSPSVGQLVAVK-AEEDAWLRAQVIEVEED-KVKVYYVDHGFSEVVERSKLFKLNKQFYS 78

                          90
                  ....*....|....*...
gi 2217263382 412 LPFQAIECSLARIAPSGD 429
Cdd:cd20427    79 LPFQATKCKLAGLEPFSD 96

rRNA processing protein Krr1/Pno1, contains KH domain [Translation, ribosomal structure and biogenesis];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDvGDerVLLISGF-PVQVCKAKAAIHQI---------------- 118
Cdd:COG1094     3 YVKIPKDRIGVLIGKGGETKKEIEEKTGVKLDIDSET-GE--VTIEPGEdPLAALKARDIVKAIgrgfspekalrllddd 79

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2217263382 119 -------LTENTPVSEQLsvpQRSVGRIIGRGGETIRSICKASGAKI 158
Cdd:COG1094    80 ymlevidLPDVGKSPNAL---DRIKGRIIGREGRTRRIIEELTGVDI 123

second Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the second one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 309 EVYVSASEHPNHFWIQIVgSRSLQLDKLVNEMTQHYENSVPE--DLTVHVGDIVAAPlPTNGSWYRARVLGTLENGNLDL 386
Cdd:cd20437     6 KVKITAAVSPSKFYCQLL-SWEPELSKLTTQMTLHYESVSKElnPSCENFGLLCAAK-GKDGQWHRGFLQQLLPPSQVKV 83

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2217263382 387 YFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 422
Cdd:cd20437    84 WFIDYGNSEAVSSHSVLKLPPDFFSLPLMSFPCSLS 119

third type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 128 QLSVPQRSVGRIIGRGGETIRSICKASGAKITCDKESE---GTllLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd09031     4 ELEVPENLVGAILGKGGKTLVEIQELTGARIQISKKGEfvpGT--RNRKVTITGTPAAVQAAQYLIEQRI 71

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2217263382  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDErVLLISGFPVQVCKAKAAI 115
Cdd:cd22411     1 SIKVPIFKQFHKNIIGKGGATIKKIREETNTRIDLPEENSDSD-VITITGKKEDVEKARERI 61

second type I K homology (KH) RNA-binding domain found in the family of neuro-oncological ventral antigen (Nova); The family includes two related neuronal RNA-binding proteins, Nova-1 and Nova-2. Nova-1, also called onconeural ventral antigen 1, or paraneoplastic Ri antigen, or ventral neuron-specific protein 1, may regulate RNA splicing or metabolism in a specific subset of developing neurons. It interacts with RNA containing repeats of the YCAY sequence. It is a brain-enriched splicing factor regulating neuronal alternative splicing. Nova-1 is involved in neurological disorders and carcinogenesis. Nova-2, also called astrocytic NOVA1-like RNA-binding protein, is a neuronal RNA-binding protein expressed in a broader central nervous system (CNS) distribution than Nova-1. It functions in neuronal RNA metabolism. NOVA family proteins contain three K-homology (KH) RNA-binding domains. The model corresponds to the second one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2217263382 131 VPQRSVGRIIGRGGETIRSICKASGAKITCDKESEGTLLLSRLIKISGTQKEVAAAKHLILEKV 194
Cdd:cd22436     7 VPNSTAGMIIGKGGATIKAIMEQSGARVQISQKPESINLQERVVTVTGEPEANRKAVSLILQKI 70

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2217263382  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGFPVQVCKAKAAIHQIL 119
Cdd:cd22398     1 GMEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDgNSPDRICVITGPPDQVQHAARMIQELI 67

third Tudor domain found in Tudor domain-containing protein 7 (TDRD7) and similar proteins; TDRD7, also called PCTAIRE2-binding protein, or Tudor repeat associator with PCTAIRE-2 (Trap), is a component of specific cytoplasmic RNA granules involved in post-transcriptional regulation of specific genes: probably acts by binding to specific mRNAs and regulating their translation. It is required for lens transparency during lens development, by regulating translation of genes such as CRYBB3 and HSPB1 in the developing lens. It is also essential for dynamic ribonucleoprotein (RNP) remodeling of chromatoid bodies during spermatogenesis. TDRD7 contains three Tudor domains. The model corresponds to the third one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 332 QLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNgsWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLS 411
Cdd:cd20429     8 KLEVLMEEMILYYNKTEERPVAIEKNKVYAAKIENN--WYRVLVKGILTNGLVSVYELDYGKHELVSIRKVQPLIEKFRQ 85

                  ....*.
gi 2217263382 412 LPFQAI 417
Cdd:cd20429    86 LPFQAI 91

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 2217263382  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDERVlLISGFPVQVCKAKAAIHQILT 120
Cdd:cd02394     5 TIEIDPKFHGHIIGKGGANIKRIREESGVSIRIPDDEANSDEI-RIEGSPEGVKKAKAEILELVD 68

first 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 first one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 2217263382  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgDERVLLISGFPVQVCKAKAAIHQILTE 121
Cdd:cd22438     1 IRMLMQGKEVGSIIGKKGETIKKFREESGARINISDGSC-PERIVTVTGTTDAVFKAFELICRKLEE 66

first Tudor domain found in Tudor domain-containing protein 15 (TDRD15) and similar proteins; TDRD15 is an uncharacterized Tudor domain-containing protein that contains seven Tudor domains. This model corresponds to the first one. The Tudor domain binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions.

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217263382 317 HPNHFWIQIVGSRSLQLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNGSWYRARVLgTLENGNLDLYFVDFGDNGD 396
Cdd:cd20436    10 HPKEVLVKFQGQYNSICELDYHILQNEIQNATKSKSSWGVGEFCLVEDTTSGEWYRGRVL-EKIDEKYEVFLIDRGEVLN 88

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2217263382 397 CPLKDLRALRSDFLSLPFQAIECSLARIAPSGDQWEEEALDEFDRLT 443
Cdd:cd20436    89 VHATNMASASGELFQLPPKAVCGIFANILPIGEKWSSTAVNYFSSLI 135