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 145312246 283 SRSLQLDKLVNEMTQHYENSVPED--LTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 360
Cdd:cd20412    1 SRSLQLDKLVQEMTQYYESEENRHtlLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                         90
                 ....*....|....*
gi 145312246 361 RSDFLSLPFQAIECS 375
Cdd:cd20412   81 RSDFLSLPFQAIECS 95

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 145312246 283 SRSLQLDKLVNEMTQHYENSVPED--LTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 360
Cdd:cd20412    1 SRSLQLDKLVQEMTQYYESEENRHtlLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                         90
                 ....*....|....*
gi 145312246 361 RSDFLSLPFQAIECS 375
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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145312246  49 GEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD---ERVLLISGFPVQASGAKIT 114
Cdd:cd22428    1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGelpERVLLIQGNPVQAQRAEEA 69

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 145312246    51 DDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVgDERVLLISGFPVQASGAK 112
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPGPGS-EERVVEITGPPENVEKAA 61

putative RNA-processing protein; Provisional

                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 145312246  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED 92
Cdd:PRK13763   4 MEYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSET 42

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 145312246 283 SRSLQLDKLVNEMTQHYENSVPED--LTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRAL 360
Cdd:cd20412    1 SRSLQLDKLVQEMTQYYESEENRHtlLTVQVGDIVAAPFRHDGSWYRARVLGFLENGNLDLYFVDYGDSGYVPLEDLRAL 80

                         90
                 ....*....|....*
gi 145312246 361 RSDFLSLPFQAIECS 375
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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145312246  49 GEDDIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD---ERVLLISGFPVQASGAKIT 114
Cdd:cd22428    1 GSRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFKDEGSGGelpERVLLIQGNPVQAQRAEEA 69

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 145312246 309 VHVGDIVAAPlpTNGSWYRARVLGTLENGNL-DLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 381
Cdd:cd20407    5 IEVGVICAAP--VMNAWYRAQVVGVFEETDEvEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

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 145312246 265 VYVSASEHPNHFWIQIVGSRSLQ-LDKLVNEMTQHYENSVPEDLTV-HVGDIVAAPLPTNGSWYRARVlgtlENGNLD-- 340
Cdd:cd20408    1 GTVTEFKNPGEFYIQIYTLEVLEsLVKLTSQLKKTYASVNNHKEYIpEVGEVCVAKYSEDQNWYRALV----QTVDVQqk 76

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 145312246 341 ---LYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGDQWEEEAL 391
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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145312246  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGDErvllisgfpvqasgakitcdkesegtlllSRLIKISGT 134
Cdd:cd00105    1 EEIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSG-----------------------------ERVVTITGT 51

                         90
                 ....*....|..
gi 145312246 135 QKEVAAAKHLIL 146
Cdd:cd00105   52 PEAVEKAKELIE 63

Tudor domain found in Tudor domain-containing protein 5 (TDRD5) and similar proteins; TDRD5 is an RNA-binding protein directly associated with piRNA precursors. It is required for retrotransposon silencing, chromatoid body assembly, and spermiogenesis. TDRD5 participates in the repression of transposable elements and prevents their mobilization, which is essential for germline integrity. TDRD5 contains three LOTUS 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 145312246 266 YVSASEHPNHFWIQIVGS-RSLQLDKLVNEMTQHYENS-------VPEDLtVHVGDIVAAPLPTNGSWYRARVLGTLENG 337
Cdd:cd20419    1 FVEYIESPSQFYVRFYSKdTSEMLEDMMIEMRRCYSNEhvseryvMPEAF-IQPGQVCCVRIPEDVWWYRVIIHQVLNKQ 79

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 145312246 338 NLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 376
Cdd:cd20419   80 EVEVFYPDFGDIGTVQKSRLRFLKCCYSKLPAQAIPASL 118

fourth 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 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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145312246 263 LEVYVSASEHPNHFWIQIVgSRSLQLDKLVNEMTQHYENSvpEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLY 342
Cdd:cd20439   12 VDVKCSYVNSPGDFWCQLQ-TKSSELKSLMKQIQSYYLIH--NDPYKHGQIACVAKYSKDGKWYRAAVLKQVSAKEVDVI 88

                         90       100       110
                 ....*....|....*....|....*....|....
gi 145312246 343 FVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 376
Cdd:cd20439   89 FVDYGNQERVLISDLRAIKPQFLLLEGQAFRCSL 122

second Tudor domain found in Tudor domain-containing protein 12 (TDRD12) and similar proteins; TDRD12, also called ES cell-associated transcript 8 protein (ECAT8), is a putative ATP-dependent DEAD-like RNA helicase that is essential for germ cell development and maintenance. It acts as a unique piRNA biogenesis factor essential for secondary PIWI interacting RNA (piRNA) biogenesis. TDRD12 contains two Tudor domains, one at the N-terminus and the other at the C-terminal end. The model corresponds to the second/C-terminal 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 145312246 272 HPNHFWIQIVG----------SRSLQLDKLVNEMTQHY---ENSVPEDlTVHVGDIVAAPLPTNgSWYRARVLGTLENG- 337
Cdd:cd20435    1 DATHYSARILEhrssdgevtkSMSSTYLKLSMKLNMYYsdpSNRILHG-KVKVGDLCAVEDENN-LYHRVKVLEITEKDd 78

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 145312246 338 -----NLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 381
Cdd:cd20435   79 ktkprEVLVKFIDEGRVETVVVSQLLELPEELKSLPPQAVEVFLCNVKP 127

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana KH domain-containing protein HEN4 and similar protein; HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. HEN4 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of HEN4.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145312246  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISGFPVQASGAK 112
Cdd:cd22462    1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVlKPDSATGERIVLISGTPDQARHAQ 59

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 145312246 322 NGSWYRARVLGTLEN-GNLDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLAR-IAPSG 383
Cdd:cd20423   16 DGKWCRALIDNVYEPvEMVEVTYVDYGNKELVSLKNLRSISEEFLKLKAQAFRCSLYNlIQPSG 79

sixth 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 sixth 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 145312246 264 EVYVSASEHPNHFWIQIVgsrslQLDKLVNEMTQHYENS--VPEDL---TVHVGDIVAAPLPTNGSWYRARVLGTLENGN 338
Cdd:cd20425    3 EVYVSHVNSPSDFYVQLA-----QDEDELSMISEKLNASkaNDEEVeceSLQLGDLICAEYPEDGLWYRAVVKEKIPNNL 77

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 145312246 339 LDLYFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSL 376
Cdd:cd20425   78 VSVQFIDYGNTSVVQPSKIHRLPKELLSIPALSIHCFL 115

sixth 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 sixth 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 145312246 273 PNHFWIQIVGSRS--LQLDKLVNEMTQHYENSVpeDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNG 350
Cdd:cd20441    2 PSRFFIQLSEDEKviLQLAEELNETSEKSRENA--AVKLKVGDLVAAEYDEDLALYRAVITAVLPGKSFKVEFIDYGNTA 79

                         90       100
                 ....*....|....*....|....*....
gi 145312246 351 DCPLKDLRALRSDFLSLPFQAIECSLARI 379
Cdd:cd20441   80 VVDKSNIYTLQEKFLSLPRLSIPCSLSGV 108

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 145312246 264 EVYVSASEHPNHFWIQIVgSRSLQLDKLVNEMTQHYENSVPE--DLTVHVGDIVAAPlPTNGSWYRARVLGTLENGNLDL 341
Cdd:cd20437    6 KVKITAAVSPSKFYCQLL-SWEPELSKLTTQMTLHYESVSKElnPSCENFGLLCAAK-GKDGQWHRGFLQQLLPPSQVKV 83

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 145312246 342 YFVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLA 377
Cdd:cd20437   84 WFIDYGNSEAVSSHSVLKLPPDFFSLPLMSFPCSLS 119

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 145312246 287 QLDKLVNEMTQHYENSVPEDLTVHVGDIVAAPLPTNgsWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFLS 366
Cdd:cd20429    8 KLEVLMEEMILYYNKTEERPVAIEKNKVYAAKIENN--WYRVLVKGILTNGLVSVYELDYGKHELVSIRKVQPLIEKFRQ 85

                 ....*.
gi 145312246 367 LPFQAI 372
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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145312246  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDtedvgdervllisgfpvqasgakitcDKESEgtlllSRLIKISGTQ 135
Cdd:cd02394    5 TIEIDPKFHGHIIGKGGANIKRIREESGVSIRIP--------------------------DDEAN-----SDEIRIEGSP 53

                         90
                 ....*....|....*
gi 145312246 136 KEVAAAKHLILEKVS 150
Cdd:cd02394   54 EGVKKAKAEILELVD 68

third 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 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
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 145312246 311 VGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFL 365
Cdd:cd20410    5 VGEPCCAFFSGDGNWYRAMVKEILPGGAVKVHFVDYGNVEEVTLDKLRKITSTFL 59

second 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 second one.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 145312246  52 DIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDV--GDERVLLISGFP 105
Cdd:cd22433    1 DCELRLLVHQSQAGCIIGRAGFKIKELREKTGATIKVYSECCprSTDRVVQIGGKP 56

Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, also called Staphylococcal nuclease domain-containing protein 1 (SND1), 100 kDa coactivator, EBNA2 coactivator p100, or p100 co-activator, is a multifunctional protein that is reportedly associated with different types of RNA molecules, including mRNA, miRNA, pre-miRNA, and dsRNA. It has been implicated in a number of biological processes in eukaryotic cells, including the cell cycle, DNA damage repair, proliferation, and apoptosis. TDRD11 is overexpressed in multiple cancers and functions as an oncogene. It contains multiple Staphylococcal nuclease (SN) domains and 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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145312246 287 QLDKLVNEMTQHYENS--VPEDLTVHVGDIVAAPLPTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDF 364
Cdd:cd20433    4 QLEKLMEKLRFEIASNppLPGSYTPRKGDLCAAKFVEDGEWYRAKVEKVEGDKKVHVLYIDYGNREVLPSTRLAALPPAF 83

Tudor domain found in Arabidopsis thaliana ribonuclease Tudor 1 (AtTudor1), ribonuclease Tudor 2 (AtTudor2), and similar proteins; The family includes AtTudor1 (also called Tudor-SN protein 1) and AtTudor2 (also called Tudor-SN protein 2 or 100 kDa coactivator-like protein). They are cytoprotective ribonucleases (RNases) required for resistance to abiotic stresses, acting as positive regulators of mRNA decapping during stress. Members of this family contain 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 145312246 276 FWIQIVGSRSL-----QLDKLVNEmtqhyENSVPED-LTVHVGDIVAAPLPTNGSWYRARVLGTLENGN------LDLYF 343
Cdd:cd20443    4 FYVQVVSDQRLssiqqQLEGLSLK-----DKANPPGgFNPKKGELVLAQFSADNSWNRAMVVNAPRQGTqspkdeYEVFY 78

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 145312246 344 VDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAP 381
Cdd:cd20443   79 IDYGNQETVPLSALRPLDPSVSSAPGLAQLCSLAHIKV 116

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 145312246  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED-VGDERVLLISGFP--VQASGAKIT 114
Cdd:cd22398    1 GMEVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDgNSPDRICVITGPPdqVQHAARMIQ 64

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        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 145312246  54 EIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIdvdtedvgdervllisGFPVQAsgakitcDKESEgtlllsrLIKISG 133
Cdd:cd22413    4 TVEIRAKPEYHRFLIGRGGANIRKIRDNTGARI----------------IFPTAR-------DEDQE-------LITIIG 53

                         90
                 ....*....|..
gi 145312246 134 TQKEVAAAKHLI 145
Cdd:cd22413   54 TKEAVEKAKEEL 65

fifth 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 fifth 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 145312246 322 NGSWYRARVLGTLENGNLDLY--FVDFGDNGDCPLKDLRALRSDFLSLPFQAIECSLARIAPSGDQWEEEaldefdRLTH 399
Cdd:cd20418   16 DGKWYRAKLLSILEFNPVKILvrHVDYGSTAALPTSRLRQIPAELMQYPCQAIKVKLAGFKPPLNDSETE------RIPY 89

                 ....
gi 145312246 400 CADW 403
Cdd:cd20418   90 CPEW 93

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
                 ....*....|....*....|....*....|....*....|
gi 145312246  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTED 92
Cdd:cd22447    4 QNLTVPIPASTRARIIGKKGANLKQIREKTGVRIDIPPRD 43

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 3 (PCBP3) and similar proteins; PCBP3, also called alpha-CP3, or PCBP3-overlapping transcript, or PCBP3-overlapping transcript 1, or heterogeneous nuclear ribonucleoprotein E3, or hnRNP E3, is a single-stranded nucleic acid binding protein that binds preferentially to oligo dC. It can function as a repressor dependent on binding to single-strand and double-stranded poly(C) sequences. PCBP3 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 145312246  56 EMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVGD-ERVLLISGFPVQASGAK 112
Cdd:cd22522   12 ELTIPNDLIGCIIGRQGTKINEIRQMSGAQIKIANATEGSsERQITITGSPANISLAQ 69

type I K homology (KH) RNA-binding domain found in polyribonucleotide nucleotidyltransferase (PNPase) and similar proteins; PNPase, also called polynucleotide phosphorylase, is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. It catalyzes the phosphorolysis of single-stranded polyribonucleotides processively in the 3'- to 5'-direction. It is also involved, along with RNase II, in tRNA processing. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. The model corresponds to the KH domain.

                         10        20        30
                 ....*....|....*....|....*....|....*
gi 145312246  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVD 89
Cdd:cd02393    6 TTIKIPPDKIGDVIGPGGKTIRAIIEETGAKIDIE 40

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
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 145312246  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDteDVGDERVLLISGFPVQASGAK 112
Cdd:cd22449    6 VKFDVPAKYVPHIIGKKGANINKLREEYGVKIDFE--DKTGEGNVEIKGSKKNVEEAK 61

fifth type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein RCF3 and similar protein; RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 contains five K-homology (KH) RNA-binding domains. The model corresponds to the KH5 domain of RCF3.

                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 145312246  53 IEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARI----DVDTEDvGDERVLLISGFPVQASGAKITCDK 117
Cdd:cd22463    2 SKIEFQIPEAVVGLIIGKSGNTIKQISERSGAFVaivqDRYPLE-ETQKILRISGTEEQLKRAQSLVEG 69

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
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145312246  55 IEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDVG-DERVLLISGFPVQASGAK 112
Cdd:cd22434    4 TQVTIPKDLAGSIIGKGGQRIRQIRHESGASIKIDEPLPGsEDRIITITGTQDQIQNAQ 62

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 145312246   310 HVGDIVAAPLpTNGSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDF 364
Cdd:smart00333   4 KVGDKVAARW-EDGEWYRARIVKVDGEQLYEVFFIDYGNEEVVPPSDLRQLPEEL 57

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH1 domain of PEPPER and FLK, as well as KH1 and KH3 domains of RCF3 and HEN4.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 145312246  52 DIEIEMRVPQEAVKLIIGRQGANIKQLRKQTGARIDV-DTEDVGDERVLLISG 103
Cdd:cd22459    1 EVVFRLLCPVSKAGSVIGKGGEIIKQLRQETGARIKVeDGVPGTEERVITISS 53

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana RNA-binding KH domain-containing protein PEPPER and similar proteins; The family includes a group of plant RNA-binding KH domain-containing proteins, such as PEPPER, flowering locus K homology domain protein (FLK), RNA-binding KH domain-containing protein RCF3 and KH domain-containing protein HEN4. PEPPER regulates vegetative and gynoecium development. It acts as a positive regulator of the central floral repressor FLOWERING LOCUS C. In concert with HUA2, PEPPER antagonizes FLK by positively regulating FLC probably at transcriptional and post-transcriptional levels, and thus acts as a negative regulator of flowering. FLK, also called flowering locus KH domain protein, regulates positively flowering by repressing FLC expression and post-transcriptional modification. PEPPER and FLK contain three K-homology (KH) RNA-binding domains. RCF3, also called protein ENHANCED STRESS RESPONSE 1 (ESR1), or protein HIGH OSMOTIC STRESS GENE EXPRESSION 5 (HOS5), or protein REGULATOR OF CBF GENE EXPRESSION 3, or protein SHINY 1 (SHI1), acts as negative regulator of osmotic stress-induced gene expression. It is involved in the regulation of thermotolerance responses under heat stress. It functions as an upstream regulator of heat stress transcription factor (HSF) genes. HEN4, also called protein HUA ENHANCER 4, plays a role in floral reproductive organ identity in the third whorl and floral determinacy specification by specifically promoting the processing of AGAMOUS (AG) pre-mRNA. It functions in association with HUA1 and HUA2. RCF3 and HEN4 contain five KH RNA-binding domains. The model corresponds to the KH2 domain of PEPPER and FLK, as well as KH2 and KH4 domains of RCF3 and HEN4.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 145312246  59 VPQEAVKLIIGRQGANIKQLRKQTGARIDVDTEDV------GDERVLLISGFPVQASGA 111
Cdd:cd22460    6 VASSQAGSLIGKGGAIIKQIREESGASVRILPEEElppcasPDDRVVQISGEAQAVKKA 64

second 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 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 145312246 323 GSWYRARVLGTLENGNLDLYFVDFGDNGDCPLKDLRALRSDFL----SLPFQAIECSLARIAPSGDQWEEEA 390
Cdd:cd20428   64 GKWARVEITNVHSSRALDVHFLDTGTVASVKVSELREIPPPFLreliSIPPQALKCCLADLPLNIGMWTPDA 135