Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains 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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907100828 555 WKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPV 607
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIKPI 53

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907100828 194 VDEKALKHITEMGFSKEASRQALMDNANNLEAALNVLLN 232
Cdd:cd14282     1 VDEKALRHITEMGFSKEAARQALMDNNNNLEAALNFLLT 39

Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains 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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907100828 555 WKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPV 607
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIKPI 53

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907100828 194 VDEKALKHITEMGFSKEASRQALMDNANNLEAALNVLLN 232
Cdd:cd14282     1 VDEKALRHITEMGFSKEAARQALMDNNNNLEAALNFLLT 39

Tudor domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907100828 556 KPGDECFALYWEDNKFYRAEVEALHSSGMtAVVKFTDYGNYEEVLLSNIKP 606
Cdd:pfam00567  49 AVGDGCVAAFSEDGKWYRAKITESLDDGL-VEVLFIDYGNTETVPLSDLRP 98

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907100828 194 VDEKALKHITEMGFSKEASRQALMDNANNLEAALNVL 230
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing proteins. In the nucleus, it acts as a coactivator; it recognizes and binds asymmetric dimethylation on the core histone tails associated with transcriptional activation (H3R17me2a and H4R3me2a) and recruits proteins at these arginine-methylated loci. In the cytoplasm, it may play a role in the assembly and/or disassembly of mRNA stress granules and in the regulation of translation of target mRNAs by binding Arg/Gly-rich motifs (GAR) in dimethylarginine-containing proteins. TDRD3 contains 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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907100828 555 WKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPV 607
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIKPI 53

UBA domain of Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is a modular protein containing Tudor domain, a DUF/OB-fold motif and a ubiquitin-associated (UBA) domain. It shows both nucleic acid- and methyl-binding properties and can interact with methylated RNA-binding proteins, such as fragile X mental retardation protein (FMRP) and DEAD/H box-3 (also known as DDX3X/Y, DBX/Y, HLP2 and DDX14) which is implicated in human genetic diseases. At this point, TDRD3 may play a central role in RNA processing regulatory pathways involving arginine methylation. TDRD3 localizes predominantly to the cytoplasm stress granules (SGs). The Tudor domain is essential and sufficient for its recruitment to SGs.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907100828 194 VDEKALKHITEMGFSKEASRQALMDNANNLEAALNVLLN 232
Cdd:cd14282     1 VDEKALRHITEMGFSKEAARQALMDNNNNLEAALNFLLT 39

Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar proteins; SPF30, also called 30 kDa splicing factor SMNrp, SMN-related protein, or survival motor neuron domain-containing protein 1 (SMNDC1), is an essential pre-mRNA splicing factor required for assembly of the U4/U5/U6 tri-small nuclear ribonucleoprotein into the spliceosome. Overexpression of SPF30 causes apoptosis. It contains 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
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907100828 555 WKPGDECFALYWEDNKFYRAEVEALHSSGmTAVVKFTDYGNYEEVLLSNIKPVQTE 610
Cdd:cd20399     1 WKVGDKCMAVWSEDGQYYEATIEEISEDG-TCTVTFDGYGNTEVTPLSQLKPREEG 55

Tudor domain found in survival motor neuron protein (SMN) and similar proteins; SMN, also called component of gems 1, or Gemin-1, is part of a multimeric SMN complex that includes spliceosomal Sm core proteins and plays a catalyst role in the assembly of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. Mutations in human SMN lead to motor neuron degeneration and spinal muscular atrophy. SMN contains a central, highly conserved Tudor domain that is required for U snRNP assembly and Sm protein binding and has been shown to bind arginine-glycine-rich motifs in an methylarginine-dependent manner.

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 1907100828 555 WKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPVQTE 610
Cdd:cd20398     1 WKVGDKCRAVYSEDGIIYEATIVSIDAERGTCVVRYTGYGNEEEQNLSDLLPPSGE 56

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 1907100828  555 WKPGDECFAlYWEDNKFYRAEVEALHSSGMtAVVKFTDYGNYEEVLLSNIKP 606
Cdd:smart00333   3 FKVGDKVAA-RWEDGEWYRARIVKVDGEQL-YEVFFIDYGNEEVVPPSDLRQ 52

Tudor domain;

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1907100828 556 KPGDECFALYWEDNKFYRAEVEALHSSGMtAVVKFTDYGNYEEVLLSNIKP 606
Cdd:pfam00567  49 AVGDGCVAAFSEDGKWYRAKITESLDDGL-VEVLFIDYGNTETVPLSDLRP 98

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1907100828 543 IESSIPVEYAKVWKPGDECFALYWEDNKFYRAEVEALhSSGMTAVVKFTDYGNYEEVLLSNIKP 606
Cdd:cd20433    16 IASNPPLPGSYTPRKGDLCAAKFVEDGEWYRAKVEKV-EGDKKVHVLYIDYGNREVLPSTRLAA 78

UBA2 domain found in Schizosaccharomyces pombe ubiquitin carboxyl-terminal hydrolase 14 (spUBP14) and similar proteins; spUBP14, also called deubiquitinating enzyme 14, UBA domain-containing protein 2, ubiquitin thioesterase 14, or ubiquitin-specific-processing protease 14, functions as a deubiquitinating enzyme that is involved in protein degradation in fission yeast. Members in this family contain two tandem ubiquitin-association (UBA) domains. This model corresponds to the UBA2 domain.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 1907100828 196 EKALKHITEMGFSKEASRQALMDNANNLEAALNVLLNSS 234
Cdd:cd14297     1 EDLVKQLVDMGFTEAQARKALRKTNNNVERAVDWLFEGP 39

Ubiquitin associated domain; Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.

                           10        20        30
                   ....*....|....*....|....*....|....*..
gi 1907100828  195 DEKALKHITEMGFSKEASRQALMDNANNLEAALNVLL 231
Cdd:smart00165   1 DEEKIDQLLEMGFSREEALKALRAANGNVERAAEYLL 37

Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1907100828 553 KVWKPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPVQTEAWEE 614
Cdd:pfam06003  67 KEWKVGDSCNAFWSEDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDED 128

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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1907100828 543 IESSIPVEYAKV-----WKP--GDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKP 606
Cdd:cd20408    28 LTSQLKKTYASVnnhkeYIPevGEVCVAKYSEDQNWYRALVQTVDVQQKKAGVFYIDYGNEETVPLNRIQP 98

Tudor domain found in DNA excision repair protein ERCC-6-like 2 (ERCC6L2) and similar proteins; ERCC6L2, also called DNA repair and recombination protein RAD26-like (RAD26L), may be involved in early DNA damage response. It regulates RNA Pol II-mediated transcription via its interaction with DNA-dependent protein kinase (DNA-PK) to resolve R loops and minimize transcription-associated genome instability. ERCC6L2 gene mutations have been associated with bone marrow failure that includes developmental delay and microcephaly. It contains an N-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
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 1907100828 555 WKPGDECFALYWEDNKFYRAEVEALHSSG---MTAVVKFTDYGNY--EEVLLSNIKPVQ 608
Cdd:cd20400     1 WHVGDRCLAPYSGDGKLYEAVIKSISTDEngkSFAVVKFLGYESDedEKVPVSKLQKVK 59

UBA/TS-N domain; This small domain is composed of three alpha helices. This family includes the previously defined UBA and TS-N domains. The UBA-domain (ubiquitin associated domain) is a novel sequence motif found in several proteins having connections to ubiquitin and the ubiquitination pathway. The structure of the UBA domain consists of a compact three helix bundle. This domain is found at the N terminus of EF-TS hence the name TS-N. The structure of EF-TS is known and this domain is implicated in its interaction with EF-TU. The domain has been found in non EF-TS proteins such as alpha-NAC and MJ0280.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907100828 194 VDEKALKHITEMGFSKEASRQALMDNANNLEAALNVL 230
Cdd:pfam00627   1 EDEEAIQRLVEMGFDREQVREALRATGNNVERAAEYL 37

UBA domain found in a putative ubiquitin conjugating enzyme from plasmodium Yoelii (pyUCE) and similar proteins; P. Yoelii ubiquitin-conjugating enzyme and other uncharacterized family members show high sequence similarity to the human Huntingtin interacting protein-2 (HIP2) which belongs to a class II E2 ubiquitin-conjugating enzyme family. These proteins may play roles in the ubiquitin-mediated protein degradation pathway. They all contain a C-terminal ubiquitin-associated (UBA) domain in addition to an N-terminal catalytic ubiquitin-conjugating enzyme E2 (UBCc) domain.

                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 1907100828 196 EKALKHITEMGFSKEASRQALMDNANNLEAALNVLL 231
Cdd:cd14314     2 EEKIKKLLEMGFPRDQARKALEKNGWDETLALNTLL 37

fifth 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 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
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1907100828 561 CFALYWEDNKFYRAEVEALHSSGMTAVVkFTDYGNYEEVLLSNIKPVQTEAWE 613
Cdd:cd20440    63 CLAKYFEDGQWYRALAHPVESSSHLSVY-FVDYGNKQIVEKNEVLPIPDTAVD 114

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907100828 557 PGDECFALY--WEDNKFYRAEVeaLHSSGMTAVVKFTDYGNYEEV---LLSNIKP 606
Cdd:cd20431    43 PNLLCLAPFtdADMKKYYRAKI--LYVSGSSAEVFFVDYGNTSQVpssLLREIPE 95

UBA domain found in trinucleotide repeat-containing gene 6C protein (TNRC6C) and similar proteins; TNRC6C is one of three GW182 paralogs in mammalian genomes. It is enriched in P-bodies and important for efficient miRNA-mediated repression. TNRC6C is composed of an N-terminal glycine/tryptophan (G/W)-rich region containing an Ago hook responsible for Ago protein-binding; a ubiquitin-associated (UBA) domain and a glutamine (Q)-rich region in the middle region; a middle G/W-rich region, a RNA recognition motif (RRM), also called RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a C-terminal G/W-rich region, at the C-terminus. A bipartite C-terminal region including the middle and C-terminal G/W-rich regions is referred as silencing domain that triggers silencing of bound transcripts by inhibiting protein expression and promoting mRNA decay via deadenylation. The C-terminal half containing the RRM domain functions as a key effector domain mediating protein synthesis repression by TNRC6C.

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 1907100828 197 KALKHITEMGFSKEASRQALMDNANNLEAALNVLL 231
Cdd:cd14283     2 RLLKQLTDMGFKREPAEEALKSNNMNLEQAVSALL 36

seventh 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 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 1907100828 556 KPGDECFALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIK 605
Cdd:cd20442    51 KEGLECLAKSKKNLKWYRAVVEHLYPETEKMLVFFVDHGITEVVSMGNIK 100

UBA domain found in Arabidopsis thaliana E3 ubiquitin-protein ligase UPL1 (atUPL1), UPL2 (atUPL2) and similar proteins; The family includes two highly similar 405-kDa HECT E3 ubiquitin-protein ligases (UPLs), UPL1 and UPL2, from Arabidopsis thaliana. The HECT E3 UPL family plays a prominent role in the ubiquitination of plant proteins. The biological functions of UPL1 and UPL2 remain unclear. Both of them contain a ubiquitin-associated (UBA) domain and a C-terminal HECT domain. UBA domain may be involved in ubiquitin metabolism. HECT domain is necessary and sufficient for their E3 catalytic activity, but requires ATP, E1 and an E2 of the Arabidopsis UBC8 family to ubiquitinate proteins.

                          10        20        30
                  ....*....|....*....|....*....|..
gi 1907100828 202 ITEMGFSKEASRQALMD-NANNLEAALNVLLN 232
Cdd:cd14327     6 LVEMGFSRERAEEALRAvGTNSVELAMEWLFT 37

Tudor domain found in PHD finger protein 20 (PHF20), PHF20-like protein 1 (PHF20L1), and similar proteins; PHF20, also called Glioma-expressed antigen 2, hepatocellular carcinoma-associated antigen 58, novel zinc finger protein, or transcription factor TZP (referring to Tudor and zinc finger domain containing protein), is a regulator of NF-kappaB activation by disrupting recruitment of PP2A to p65. It also functions as a transcription factor that binds to Akt and plays a role in Akt cell survival/growth signaling. Moreover, it transcriptionally regulates p53. The phosphorylation of PHF20 on Ser291 mediated by protein kinase B (PKB) is essential in tumorigenesis via the regulation of p53-mediated signaling. PHF20L1 is an active malignant brain tumor (MBT) domain-containing protein that binds to monomethylated lysine 142 on DNA (cytosine-5) Methyltransferase 1 (DNMT1) (DNMT1K142me1) and colocalizes at the perinucleolar space in a SET7-dependent manner. Both PHF20 and PHF20L1 contain an N-terminal malignant brain tumor (MBT) domain, a Tudor domain, a plant homeodomain (PHD) finger and putative DNA-binding domains AT hook and C2H2-type zinc finger. 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 1907100828 555 WKPGDECFAlYWEDNKFYRAEVEALHSSGmTAVVKFTDyGNYEEVLLSNIKP 606
Cdd:cd20386     1 FKVGEEVLA-RWSDCKFYPAKILKVLDNG-TYEVLFYD-GFKKTVKASNLKK 49

UBA domain found in yeast UBA domain-containing protein RUP1p and similar proteins; RUP1p is a ubiquitin-associated (UBA) domain-containing protein encoded by a nonessential yeast gene RUP1. It can mediate the association of Rsp5 and Ubp2. The N-terminal UBA domain is responsible for antagonizing Rsp5 function, as well as bridging the Rsp5-Ubp2 interaction. No other characterized functional domains or motifs are found in RUP1p.

                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1907100828 196 EKALKHITEMGFSKEASRQALMDNANNLEAALNVLLN 232
Cdd:cd14307     1 EEAVASLLEMGIPREVAIEALRETNGDVEAAANYIFS 37

UBA1 domain found in NEDD8 ultimate buster 1 (NUB1) and similar proteins; NUB1, also called negative regulator of ubiquitin-like proteins 1, renal carcinoma antigen NY-REN-18, or protein BS4, is a NEDD8-interacting protein that can be induced by interferon. It functions as a strong post-transcriptional down-regulator of the NEDD8 expression and plays critical roles in regulating many biological events, such as cell growth, NF-kappaB signaling, and biological responses to hypoxia. NUB1 can also interact with aryl hydrocarbon receptor-interacting protein-like 1 (AIPL1) which may function in the regulation of cell cycle progression. NUB1 contains three ubiquitin-associated domains (UBA), a bipartite nuclear localization signal (NLS) and a PEST motif. This model corresponds to UBA1 domain.

                          10        20        30
                  ....*....|....*....|....*....|....
gi 1907100828 195 DEKALKHITEMGFSKEASRQALMDNANNLEAALN 228
Cdd:cd14291     1 DEDKLQQLMEMGFSEAEARLALRACNGNVERAVD 34

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
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 1907100828 556 KPGDECfALYWEDNKFYRAEVEALHSSGMTAVVKFTDYGNYEEVLLSNIKPVQTE 610
Cdd:cd20421    62 KLGSPC-AARGSDGRWYRAVLQQVFSANRVVEVLHVDYGRKEVVSVSNLRYLAPE 115