type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1634229991 609 IWEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLIGKKFK 676
Cdd:cd22395     1 VYEFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIRKKFP 68

ribonuclease Y;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229991 181 GYPVVPAEKRSSGERARETG-GAEGTGDAVLGEKVLEEALLSREHVLELENSKGPSLasLEGEEDKGKSSSSQvvgpvqE 259
Cdd:PRK00106   18 GYVLISIKMKSAKEAAELTLlNAEQEAVNLRGKAERDAEHIKKTAKRESKALKKELL--LEAKEEARKYREEI------E 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229991 260 EEYVAEKLPSRFIESAHTELAKddaapappvadakaqdrgvegelgneeSLDRNEEGLDRNEEGLDRNEESL-------D 332
Cdd:PRK00106   90 QEFKSERQELKQIESRLTERAT---------------------------SLDRKDENLSSKEKTLESKEQSLtdkskhiD 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1634229991 333 RNEEGLDRNEEIKRAAFQIISQV-ISEATEQVLATTVGK----VAGRVCQASQ 380
Cdd:PRK00106  143 EREEQVEKLEEQKKAELERVAALsQAEAREIILAETENKltheIATRIREAER 195

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1634229991 609 IWEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLIGKKFK 676
Cdd:cd22395     1 VYEFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIRKKFP 68

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 1634229991 609 IWEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLI 671
Cdd:pfam00013   1 TVEILVPSSLVGLIIGKGGSNIKEIREETGAKIQIPPSESEGNERIVTITGTPEAVEAAKALI 63

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1634229991  606 DLIIWEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYIStlPYTQSVQICHIEGSQHHVDKALNLIGKK 674
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIP--GPGSEERVVEITGPPENVEKAAELILEI 67

ribonuclease Y;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229991 181 GYPVVPAEKRSSGERARETG-GAEGTGDAVLGEKVLEEALLSREHVLELENSKGPSLasLEGEEDKGKSSSSQvvgpvqE 259
Cdd:PRK00106   18 GYVLISIKMKSAKEAAELTLlNAEQEAVNLRGKAERDAEHIKKTAKRESKALKKELL--LEAKEEARKYREEI------E 89

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229991 260 EEYVAEKLPSRFIESAHTELAKddaapappvadakaqdrgvegelgneeSLDRNEEGLDRNEEGLDRNEESL-------D 332
Cdd:PRK00106   90 QEFKSERQELKQIESRLTERAT---------------------------SLDRKDENLSSKEKTLESKEQSLtdkskhiD 142

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1634229991 333 RNEEGLDRNEEIKRAAFQIISQV-ISEATEQVLATTVGK----VAGRVCQASQ 380
Cdd:PRK00106  143 EREEQVEKLEEQKKAELERVAALsQAEAREIILAETENKltheIATRIREAER 195

type I K homology (KH) RNA-binding domain found in mitochondrial A-kinase anchor protein 1 (AKAP1) and similar proteins; AKAP1, also called A-kinase anchor protein 149 kDa, or AKAP 149, or dual specificity A-kinase-anchoring protein 1, or D-AKAP-1, or protein kinase A-anchoring protein 1 (PRKA1), or spermatid A-kinase anchor protein 84, or S-AKAP84, is a novel developmentally regulated A kinase anchor protein of male germ cells. It binds to type I and II regulatory subunits of protein kinase A and anchors them to the cytoplasmic face of the mitochondrial outer membrane.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1634229991 609 IWEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLIGKKFK 676
Cdd:cd22395     1 VYEFEVPSELVGRLIGKQGRNVKQLKQKSGAKIYIKPHPYTQNFQICSIEGTQQQIDKALKLIRKKFP 68

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 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLI 671
Cdd:cd00105     2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELI 62

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1634229991 610 WEIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLI 671
Cdd:cd22462     1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLI 62

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 1634229991 739 LDQQMYLCYSQPGIPTLPTPVEITVICAAPGADGAWWRAQVVASyeETNEVEIRYVDYGGYKRVKVDVLRQIRSDFVTLP 818
Cdd:cd20427     3 MEDEMKEFYSKSSTAMCLRSPSVGQLVAVKAEEDAWLRAQVIEV--EEDKVKVYYVDHGFSEVVERSKLFKLNKQFYSLP 80

                          90
                  ....*....|....*..
gi 1634229991 819 FQGAEVLLDSVMPLSDD 835
Cdd:cd20427    81 FQATKCKLAGLEPFSDD 97

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 1634229991 719 NAGHLFVQ----------QHTHPTFHALR-SLDQQMYlcYSQPGIPTLPTPVEITVICAAPGADGAWWRAQVVASYEETN 787
Cdd:cd20435     1 DATHYSARilehrssdgeVTKSMSSTYLKlSMKLNMY--YSDPSNRILHGKVKVGDLCAVEDENNLYHRVKVLEITEKDD 78

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 1634229991 788 -----EVEIRYVDYGGYKRVKVDVLRQIRSDFVTLPFQGAEVLLDSVMPLsDDD 836
Cdd:cd20435    79 ktkprEVLVKFIDEGRVETVVVSQLLELPEELKSLPPQAVEVFLCNVKPV-DND 131

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 1634229991 765 CAAPGADGAWWRAQVVaSYEETNEVEIRYVDYGGYKRVKVDVLRQIRSDFVTLPFQGAEVLLDSVMP 831
Cdd:cd20415    31 CVALFEDGAWYRARII-GLPGHREVEVKYVDFGNTATVTIKHVRKIKDDFLSLPEKARECRLAFIEP 96

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 1634229991 736 LRSLDQQMYLCYSQPGIPTLPTPVEITVICAAPGADGAWWRAqVVASYEETNEVEIRYVDYGGYKRVKVDVLRQIRSDFV 815
Cdd:cd20437    29 LSKLTTQMTLHYESVSKELNPSCENFGLLCAAKGKDGQWHRG-FLQQLLPPSQVKVWFIDYGNSEAVSSHSVLKLPPDFF 107

                  ...
gi 1634229991 816 TLP 818
Cdd:cd20437   108 SLP 110

second 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 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 1634229991 707 GITVEVIVVNQVNAGHLFVQQHTHPtfHALRSLDQQMYLCY-SQPGIPTLPTPVEITVICAAPGADGAWWRAQVVASYEE 785
Cdd:cd20421    10 GVTETVVVTEVTDPHRIFCQLRSLS--QELKRLSESMHQYYeGRVGSGYETRPEKLGSPCAARGSDGRWYRAVLQQVFSA 87

                          90       100       110
                  ....*....|....*....|....*....|...
gi 1634229991 786 TNEVEIRYVDYGGYKRVKVDVLRQIRSDFVTLP 818
Cdd:cd20421    88 NRVVEVLHVDYGRKEVVSVSNLRYLAPEYFRMP 120

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 1634229991 765 CAAPGADGAWWRAQVVaSYEETNEVEI--RYVDYGGYKRVKVDVLRQIRSDFVTLPFQGAEVLLDSVMPLSDDDQ----- 837
Cdd:cd20418    10 CLAEYSDGKWYRAKLL-SILEFNPVKIlvRHVDYGSTAALPTSRLRQIPAELMQYPCQAIKVKLAGFKPPLNDSEterip 88

                          90
                  ....*....|...
gi 1634229991 838 FSPE-ADAAMSEM 849
Cdd:cd20418    89 YCPEwSMKALWAM 101

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 1634229991 702 LMLPDGITVEVIVVNQVNAGHLFVQQHTHPtfHALRSLDQQM---YLCYSQPGIPTlptpveiTVICAAP-GADGAWWRA 777
Cdd:cd20439     4 YLFKPGSVVDVKCSYVNSPGDFWCQLQTKS--SELKSLMKQIqsyYLIHNDPYKHG-------QIACVAKySKDGKWYRA 74

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1634229991 778 QVVaSYEETNEVEIRYVDYGGYKRVKVDVLRQIRSDFVTLPFQ 820
Cdd:cd20439    75 AVL-KQVSAKEVDVIFVDYGNQERVLISDLRAIKPQFLLLEGQ 116

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 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLIGK 673
Cdd:cd22396     4 EYKVPDKMVGLIIGRGGEQINRLQAESGAKIQIAPDSGGLPERPCTLTGTPDAIETAKRLIDQ 66

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 1634229991 619 VGRLIGKQGRYVSFLKQTSGAKIYIS--TLPYtqsvQICHIEGSQHHVDKALNLIGKKFKE 677
Cdd:cd22438    10 VGSIIGKKGETIKKFREESGARINISdgSCPE----RIVTVTGTTDAVFKAFELICRKLEE 66

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1634229991 615 PKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSV---QICHIEGSQHHVDKALNLIGKKFKE 677
Cdd:cd22401     7 HNNLCGRLIGKDGRNIKKIMEDTNTKITISSLQDLTSYnpeRTITIKGSLEAMSEAESLISEKLRE 72

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 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLIGKKFKE 677
Cdd:cd22404     4 KVTVPNSAISRVIGRGGCNINAIREVSGAHIEIDKQKGEQGDRRITIKGSADATRQAAQLINALIKD 70

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 1634229991 714 VVNQVNAGHLFVQQHTHPTFHALRSLDQQMYLCYSQPG-IPTLPTP----VEITVICAAPGADGAWWRAQVVASYEETnE 788
Cdd:cd20419     2 VEYIESPSQFYVRFYSKDTSEMLEDMMIEMRRCYSNEHvSERYVMPeafiQPGQVCCVRIPEDVWWYRVIIHQVLNKQ-E 80

                          90       100       110
                  ....*....|....*....|....*....|..
gi 1634229991 789 VEIRYVDYGGYKRVKVDVLRQIRSDFVTLPFQ 820
Cdd:cd20419    81 VEVFYPDFGDIGTVQKSRLRFLKCCYSKLPAQ 112

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        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1634229991 614 VPKHLVGRLIGKQGRYVSFLKQTSGAKIYIST---LPYTQSV--QICHIEGSQHHVDKALNLIGK 673
Cdd:cd22460     6 VASSQAGSLIGKGGAIIKQIREESGASVRILPeeeLPPCASPddRVVQISGEAQAVKKALELVSS 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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLI 671
Cdd:cd22398     3 EVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFKPDDGNSPDRICVITGPPDQVQHAARMI 63

third type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein BTR1 and similar proteins; BTR1, also called Binding to ToMV RNA 1, is a negative regulator of tomato mosaic virus (ToMV) multiplication but has no effect on the multiplication of cucumber mosaic virus (CMV). BTR1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1634229991 612 IEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYIST----LPYTQSVQIChIEGSQHHVDKALNLIGKK 674
Cdd:cd22514     5 IGVPDEHIGAILGRGGRTINEIQQHSGARIKISDrgdfVSGTRNRKVT-ITGPQDAVQMAQYLLEQK 70

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 2 (IGF2BP2) and similar proteins; IGF2BP2, also called IGF2 mRNA-binding protein 2 (IMP-2), or hepatocellular carcinoma autoantigen p62, or IGF-II mRNA-binding protein 2, or VICKZ family member 2 (VICKZ2), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It also binds to beta-actin/ACTB and MYC transcripts. IGF2BP2 can form homooligomers and heterooligomers with IGF2BP1 and IGF2BP3 in an RNA-dependent manner. It contains 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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1634229991 618 LVGRLIGKQGRYVSFLKQTSGAKIYISTLpytQSVQICH------IEGSQHHVDKALNLIGKKFKE 677
Cdd:cd22494    10 LVGRLIGKEGRNLKKIEQDTGTKITISSL---QDLTIYNpertitVKGSIEACSSAEVEIMKKLRE 72

RNase Y N-terminal region;

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1634229991 307 EESLDRNEEGLDRNEEGLDRNEESLDRNEEGLDRNEE-------IKRAAFQIISQVISEATEQVLATTV 368
Cdd:pfam12072  91 EETLDRKDESLEKKEESLEKKEKELEAQQQQLEEKEEeleelieEQRQELERISGLTSEEAKEILLDEV 159

second type I K homology (KH) RNA-binding domain found in insulin-like growth factor 2 mRNA-binding protein 1 (IGF2BP1) and similar proteins; IGF2BP1, also called IGF2 mRNA-binding protein 1 (IMP-1), or coding region determinant-binding protein (CRD-BP), or IGF-II mRNA-binding protein 1, or VICKZ family member 1 (VICKZ1), or zipcode-binding protein 1 (ZBP-1), is an RNA-binding factor that recruits target transcripts to cytoplasmic protein-RNA complexes (mRNPs). It functions by binding to the 5' UTR of the insulin-like growth factor 2 (IGF2) mRNA and regulating IGF2 translation. It regulates localized beta-actin/ACTB mRNA translation, a crucial process for cell polarity, cell migration and neurite outgrowth. IGF2BP1 can form homodimers and heterodimers with IGF2BP1 and IGF2BP3. It contains 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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229991 613 EVP------KHLVGRLIGKQGRYVSFLKQTSGAKIYISTLP----YTQSVQIChIEGSQHHVDKALNLIGKKFKELNLTN 682
Cdd:cd22493     4 EVPlkilahNNFVGRLIGKEGRNLKKVEQDTETKITISPLQdltlYNPERTIT-VKGSIEACCRAEQEIMKKVREAYEND 82

                          90
                  ....*....|....
gi 1634229991 683 IYAPPLPSLALPSL 696
Cdd:cd22493    83 VAAMNLQSHLIPGL 96

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1634229991 734 HALRSLDQQMYLCYSQpgIPTLPTPVEITVICAAPgADGAWWRAqVVASYEETNEVEIRYVDYGGYKRVKVDVLRQIRSD 813
Cdd:cd20429     7 HKLEVLMEEMILYYNK--TEERPVAIEKNKVYAAK-IENNWYRV-LVKGILTNGLVSVYELDYGKHELVSIRKVQPLIEK 82

                  ....*...
gi 1634229991 814 FVTLPFQG 821
Cdd:cd20429    83 FRQLPFQA 90

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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYT--QSVQICHIEGSQHHVDKALNLI 671
Cdd:cd22463     5 EFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPleETQKILRISGTEEQLKRAQSLV 67

third type I K homology (KH) RNA-binding domain found in poly(rC)-binding protein 1 (PCBP1) and similar proteins; The family includes PCBP1 (also called alpha-CP1, or heterogeneous nuclear ribonucleoprotein E1, or hnRNP E1, or nucleic acid-binding protein SUB2.3) and PCBP2 (also called alpha-CP2, or heterogeneous nuclear ribonucleoprotein E2, or hnRNP E2). They are single-stranded nucleic acid binding proteins that bind preferentially to oligo dC. They act as iron chaperones for ferritin. In case of infection by poliovirus, PCBP1 plays a role in initiation of viral RNA replication in concert with the viral protein 3CD. PCBP2 is a major cellular poly(rC)-binding protein. It also binds poly(rU). PCBP2 negatively regulates cellular antiviral responses mediated by MAVS signaling. It acts as an adapter between MAVS and the E3 ubiquitin ligase ITCH, therefore triggering MAVS ubiquitination and degradation. PCBP2 forms a metabolon with the heme oxygenase 1/cytochrome P450 reductase complex for heme catabolism and iron transfer. Both PCBP1 and PCBP2 contain three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLI 671
Cdd:cd22521     8 ELTIPNDLIGCIIGRQGAKINEIRQMSGAQIKIANPVEGSTDRQVTITGSAASISLAQYLI 68

first type I K homology (KH) RNA-binding domain found in far upstream element-binding protein 3 (FUBP3) and similar proteins; 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. FUBP3 contains four K-homology (KH) RNA-binding domains. The model corresponds to the first one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1634229991 611 EIEVPKHLVGRLIGKQGRYVSFLKQTSGAKIYISTLPYTQSVQICHIEGSQHHVDKALNLIGK 673
Cdd:cd22480     4 EYKVPDKMVGFIIGRGGEQISRIQLESGCKIQIAPDSGGMPERPCVLTGTPESIEQAKRLLGQ 66