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 1912352075 711 LPTPVEVGIICAAPGLdGAWLRAQVISYFEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDNVVP 787
Cdd:cd20407     1 LPEPIEVGVICAAPVM-NAWYRAQVVGVFEETDEVEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

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 1912352075 711 LPTPVEVGIICAAPGLdGAWLRAQVISYFEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDNVVP 787
Cdd:cd20407     1 LPEPIEVGVICAAPVM-NAWYRAQVVGVFEETDEVEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

Tudor domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912352075 665 TVEVVVAHQVDAGHMFLQQHthPTFHVLRSLDQQMFACYSQPEiPTLPTPVEVGIICAAPGLDGAWLRAQvISYFEETDE 744
Cdd:pfam00567   2 TIDVVVSHIESPSTFYIQPK--SDSKKLEKLTEELQEYYASKP-PESLPPAVGDGCVAAFSEDGKWYRAK-ITESLDDGL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1912352075 745 VELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDN 784
Cdd:pfam00567  78 VEVLFIDYGNTETVPLSDLRPLPPELESLPPQAIKCQLAG 117

K homology RNA-binding domain;

                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1912352075  561 DFVIWEIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVStlPYFRDSQVCHIEGTSHQVEKVLSLIGKK 629
Cdd:smart00322   1 DPVTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIP--GPGSEERVVEITGPPENVEKAAELILEI 67

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 1912352075 711 LPTPVEVGIICAAPGLdGAWLRAQVISYFEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDNVVP 787
Cdd:cd20407     1 LPEPIEVGVICAAPVM-NAWYRAQVVGVFEETDEVEIKYLDYGGYERVPVDDLRQIRSDFMTLPFQATECYLANIEP 76

Tudor domain;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912352075 665 TVEVVVAHQVDAGHMFLQQHthPTFHVLRSLDQQMFACYSQPEiPTLPTPVEVGIICAAPGLDGAWLRAQvISYFEETDE 744
Cdd:pfam00567   2 TIDVVVSHIESPSTFYIQPK--SDSKKLEKLTEELQEYYASKP-PESLPPAVGDGCVAAFSEDGKWYRAK-ITESLDDGL 77

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 1912352075 745 VELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDN 784
Cdd:pfam00567  78 VEVLFIDYGNTETVPLSDLRPLPPELESLPPQAIKCQLAG 117

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 1912352075 694 SLDQQMFacYSQPEIPTLPTPVEVGIICAAPGLDGAWLRAQVISYFEETD-----EVELKYVDYGGYDKVKVDTLRQIRS 768
Cdd:cd20435    31 SMKLNMY--YSDPSNRILHGKVKVGDLCAVEDENNLYHRVKVLEITEKDDktkprEVLVKFIDEGRVETVVVSQLLELPE 108

                          90       100
                  ....*....|....*....|....
gi 1912352075 769 DFLTLPFQGAEVLLDNVVPlPDED 792
Cdd:cd20435   109 ELKSLPPQAVEVFLCNVKP-VDND 131

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 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVSTLPYFRDSQVCHIEGTSHQVEKVLSLI 626
Cdd:cd00105     2 EIEVPSELVGLIIGKGGSTIKEIEEETGARIQIPKEGEGSGERVVTITGTPEAVEKAKELI 62

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        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1912352075 695 LDQQMFACYSQPEIPTLPT--PVEvGIICAAPGLDGAWLRAQVISyFEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLT 772
Cdd:cd20415     4 LTKKIQEFYKEGDDGGLEIlcPVQ-GQACVALFEDGAWYRARIIG-LPGHREVEVKYVDFGNTATVTIKHVRKIKDDFLS 81

                          90
                  ....*....|....*
gi 1912352075 773 LPFQGAEVLLDNVVP 787
Cdd:cd20415    82 LPEKARECRLAFIEP 96

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 1912352075 565 WEIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVSTLPYFRDSQVCHIEGTSHQVEKVLSLI 626
Cdd:cd22462     1 IEILIPAHAVGSVIGRGGSNINQIREISGAKVEVLKPDSATGERIVLISGTPDQARHAQNLI 62

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 1912352075 677 GHMFLQQHTHPTFHVLRSLDQQMFACYSQPEIPTLPTPvEVGIICAAP-GLDGAWLRAQVisyfEETDEVELK----YVD 751
Cdd:cd20408    10 GEFYIQIYTLEVLESLVKLTSQLKKTYASVNNHKEYIP-EVGEVCVAKySEDQNWYRALV----QTVDVQQKKagvfYID 84

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 1912352075 752 YGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDNVVPLPdeDHFSPEA 798
Cdd:cd20408    85 YGNEETVPLNRIQPLKKDIELFPPCAIKCCLANVKPPS--GSWSEEC 129

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 1912352075 663 GVTVEVVVAHQVDAG----HMFLQQHThptfhvLRSLDQQMFACYSQPEIPTLPTPVEVGIICAAPGLDGAWLRAqVISY 738
Cdd:cd20437     2 GTTEKVKITAAVSPSkfycQLLSWEPE------LSKLTTQMTLHYESVSKELNPSCENFGLLCAAKGKDGQWHRG-FLQQ 74

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 1912352075 739 FEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLP 774
Cdd:cd20437    75 LLPPSQVKVWFIDYGNSEAVSSHSVLKLPPDFFSLP 110

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 1912352075 720 ICAAP-GLDGAWLRAQVISYFEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQGAEVLLDNVVP 787
Cdd:cd20423     8 VCLAKySEDGKWCRALIDNVYEPVEMVEVTYVDYGNKELVSLKNLRSISEEFLKLKAQAFRCSLYNLIQ 76

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 1912352075 717 VGIICAAP-GLDGAWLRAQVISYFEEtDEVELKYVDYGGYDKVKVDTLRQI 766
Cdd:cd20379     1 VGDLCAAKyEEDGKWYRARVLEVLSN-DKVEVFFVDYGNTETVPLSDLRPL 50

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVS----TLPYFRDSQVChIEGTSHQVEKVLSLIGKK 629
Cdd:cd09031     4 ELEVPENLVGAILGKGGKTLVEIQELTGARIQISkkgeFVPGTRNRKVT-ITGTPAAVQAAQYLIEQR 70

second 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 second one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVSTLPYFRDSQV--CHIEGTSHQVEKVLSLIGKKFKE 632
Cdd:cd22429     5 ELHVPQRAVGRIIGRGGETIRSICRTSGAKVKCDRESDDTLDLVrlITITGTKKEVDAAKSLILEKVSE 73

Tudor domain found in Tudor domain-containing protein 9 (TDRD9) and similar proteins; TDRD9 is an ATP-dependent DEAD-like RNA helicase required during spermatogenesis. It is involved in the biosynthesis of PIWI-interacting RNAs (piRNAs). A recessive deleterious mutation mutation in TDRD9 causes non-obstructive azoospermia in infertile men. TDRD9 contains an N-terminal HrpA-like RNA helicase module and a 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 1912352075 672 HQVDAGHMFLQQHTHPTFHVLRSLDQQMFACYSQPeIPTLPTPvevGIICAAPGLDGA---WLRAQVISYFeeTDEVELK 748
Cdd:cd20431     2 EVVEVGHFWGYRIDENSSEILQQLTAEINQRQLVP-LTTKPVP---NLLCLAPFTDADmkkYYRAKILYVS--GSSAEVF 75

                          90       100
                  ....*....|....*....|....*.
gi 1912352075 749 YVDYGGYDKVKVDTLRQIRSDFLTLP 774
Cdd:cd20431    76 FVDYGNTSQVPSSLLREIPETLLTLP 101

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 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVSTLPYF--RDSQVCHIEGTSHQVEKVLSLI 626
Cdd:cd22463     5 EFQIPEAVVGLIIGKSGNTIKQISERSGAFVAIVQDRYPleETQKILRISGTEEQLKRAQSLV 67

third 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 third one.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYVS 599
Cdd:cd22439     5 EITIPNDLIGCIIGKGGTKINEIRQLSGATIKIA 38

fourth 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 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1912352075 702 CYSQPEIPTL-PTPVEvgIICAAPGLDGAWLRAQVISyfEETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQ 776
Cdd:cd20411    37 CSKQSVPQQFrPRIGD--ACCARFTGDKNWYRAVVLE--TSDSEVKVLYADYGNTETLPLSRILPITKSHLELPFQ 108

third type I K homology (KH) RNA-binding domain found in Schizosaccharomyces pombe RNA-binding protein Rnc1 and similar proteins; Rnc1, also called RNA-binding protein that suppresses calcineurin deletion 1, is an RNA-binding protein that acts as an important regulator of the posttranscriptional expression of the MAPK phosphatase Pmp1 in fission yeast. It binds and stabilizes pmp1 mRNA and hence acts as a negative regulator of pmk1 signaling. Overexpression of Rnc1 suppresses the Cl(-) sensitivity of calcineurin deletion. The nuclear export of Rnc1 requires mRNA-binding ability and the mRNA export factor Rae1. Rnc1 contains three K-homology (KH) RNA-binding domains. The model corresponds to the third one.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1912352075 567 IEVPKELVGRLIGKQGRFMSYLRQASGAKIYVSTLPY-FRDSQVCHIEGTSHQVEKVLSLI 626
Cdd:cd22457     3 ISIPPDMVGCIIGKGGSKIQEIRRLSGCKISIAKAPHdETGERMFTITGTPEANDRALRLL 63

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 1912352075 560 PDFVIWEIEVPKELVGRLIGKQGRFMSYLRQASGAKIYV--STLPYFRDSQVCHIEGTSHQV----EKVLSLI 626
Cdd:cd22428     2 SRQIEIEMKVPREAVGLIIGRQGATIKQIQKETGARIDFkdEGSGGELPERVLLIQGNPVQAqraeEAIHQII 74

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
                  ....*....|....*....|....*....|....*....|....*....
gi 1912352075 567 IEVPKELVGRLIGKQGRFMSYLRQASGAKIYVSTLPYFRDSQVCHIEGT 615
Cdd:cd22459     6 LLCPVSKAGSVIGKGGEIIKQLRQETGARIKVEDGVPGTEERVITISSS 54

second 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 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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1912352075 717 VGIICAAP-GLDGAWLRAQVISYFEEtDEVELKYVDYGGYDKVKVDTLRQIRSDFL 771
Cdd:cd20409    28 VGEVCCAQfTEDNQWYRASVLAYSSE-DSVLVGYIDFGNSEEVALSRLRPIPPSLL 82

fifth 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 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.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1912352075 707 EIPTLPTPVEVGIICAAPGLDGAWLRAQVISYFEETdevELKYVDYGGYDKVKVDTLRQIRSD---FLTLPFQ 776
Cdd:cd20424    51 EIRKLELSVNPGTLCLAKYSDQHWYRGIIITNKNST---EVFFVDYGNTEKVEKEDMLPIPSDayeLLLLPMQ 120

fourth 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 fourth one.

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                  ....*....|....*....|....*....|....*....|....*....|..
gi 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYV--STLPYFRDSQVCHIEGT 615
Cdd:cd22403     3 EIRVPSSMVGRIIGKGGQNVRELQRLTGAIIKLprDQTPDEGDEVPVEIIGN 54

first 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 first one.

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                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1912352075 569 VPKELVGRLIGKQGRFMSYLRQASGAKIYVS-TLPYFRDSQ--VCHIEGTSHQVEKVLSLIGKKFK 631
Cdd:cd22435     8 VPNYAAGSIIGKGGQTIAQLQKETGARIKLSkNNDFYPGTTerVCLIQGEVEAVNAVLDFILEKIR 73

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 1912352075 690 HVLRSLDQQMFACYSQPEIPTLPtpVEVGIICAAPgLDGAWLRAQV--------ISYFEetdevelkyVDYGGYDKVKVD 761
Cdd:cd20429     7 HKLEVLMEEMILYYNKTEERPVA--IEKNKVYAAK-IENNWYRVLVkgiltnglVSVYE---------LDYGKHELVSIR 74

                          90
                  ....*....|....*.
gi 1912352075 762 TLRQIRSDFLTLPFQG 777
Cdd:cd20429    75 KVQPLIEKFRQLPFQA 90

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.

                          10        20
                  ....*....|....*....|....*.
gi 1912352075 573 LVGRLIGKQGRFMSYLRQASGAKIYV 598
Cdd:cd22386    20 VRGKLIGPGGSNVKHIQQETGAKVQL 45

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 1912352075 566 EIEVPKELVGRLIGKQGRFMSYLRQASGAKIYV----STLPyfrdSQVCHIEGTSHQVEKVLSLI 626
Cdd:cd22398     3 EVPVPRFAVGVVIGKGGEMIKKIQNETGARVQFkpddGNSP----DRICVITGPPDQVQHAARMI 63

type II K-homology (KH) RNA-binding domain found in Bacillus subtilis UPF0109 protein YlqC and similar proteins; The family includes a group of uncharacterized proteins which show sequence similarity to Bacillus subtilis UPF0109 protein YlqC. They are mainly found in bacteria and contain only one canonical type II K-homology (KH) domain that has the signature motif GXXG (where X represents any amino acid).

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                  ....*....|....*....|....*....|....*...
gi 1912352075 561 DFVIWEIEVPKELVGRLIGKQGRFMSYLRQ---ASGAK 595
Cdd:cd22533    28 KTTVYELRVAPEDVGRVIGKQGRTAKAIRTlvsAAAAK 65

seventh 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 seventh 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 1912352075 727 DGAWLRAQVISYfeETDEVELKYVDYGGYDKVKVDTLRQIRSDFLTLPFQ 776
Cdd:cd20426    60 DNHWYRALVTKI--NDNLVSVRFVDYGNEEDVVREQVRALPSELLKIPVQ 107