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Conserved domains on  [gi|2217357027|ref|XP_047273572|]
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survival motor neuron protein isoform X3 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SMN super family cl26992
Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor ...
 26-259 5.19e-89

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.


The actual alignment was detected with superfamily member pfam06003:

Pssm-ID: 428716 [Multi-domain]  Cd Length: 264  Bit Score: 264.56  E-value: 5.19e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWS 103
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027 104 EDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESqvSTDESENS-RSPGNKSDN 182
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETES--STDESDRSsGSAKHKSKS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027 183 --IKPKSAPWN-SFLPPPPPMPGPRLGPGKIIPPPPPI---------------------CPDSLDDADALGSMLISWYMS 238
Cdd:pfam06003 159 nfPMGPPSPWNpSFPPGPPPPPPGFGRHGEKPRTLGPFlsgwpppfplgppmipppppmSPDFGEDDEALGSMLIAWYMS 238

                         250       260
                  ....*....|....*....|....
gi 2217357027 239 GYHTGYYMGFRQNQKE---GRCSH 259
Cdd:pfam06003 239 GYHTGYYLGLKQGRMEaaaSKKSH 262
 
Name Accession Description Interval E-value
SMN pfam06003
Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor ...
 26-259 5.19e-89

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.


Pssm-ID: 428716 [Multi-domain]  Cd Length: 264  Bit Score: 264.56  E-value: 5.19e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWS 103
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027 104 EDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESqvSTDESENS-RSPGNKSDN 182
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETES--STDESDRSsGSAKHKSKS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027 183 --IKPKSAPWN-SFLPPPPPMPGPRLGPGKIIPPPPPI---------------------CPDSLDDADALGSMLISWYMS 238
Cdd:pfam06003 159 nfPMGPPSPWNpSFPPGPPPPPPGFGRHGEKPRTLGPFlsgwpppfplgppmipppppmSPDFGEDDEALGSMLIAWYMS 238

                         250       260
                  ....*....|....*....|....
gi 2217357027 239 GYHTGYYMGFRQNQKE---GRCSH 259
Cdd:pfam06003 239 GYHTGYYLGLKQGRMEaaaSKKSH 262
Tudor_SMN cd20398
Tudor domain found in survival motor neuron protein (SMN) and similar proteins; SMN, also ...
 92-147 2.73e-31

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.


Pssm-ID: 410469  Cd Length: 56  Bit Score: 110.05  E-value: 2.73e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2217357027  92 WKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICE 147
Cdd:cd20398     1 WKVGDKCRAVYSEDGIIYEATIVSIDAERGTCVVRYTGYGNEEEQNLSDLLPPSGE 56
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 90-147 3.25e-12

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).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 59.98  E-value: 3.25e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2217357027   90 QQWKVGDKCSAIWsEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDLLSPICE 147
Cdd:smart00333   1 PTFKVGDKVAARW-EDGEWYRARIVKVD-GEQLYEVFFIDYGNEEVVPPSDLRQLPEE 56
 
Name Accession Description Interval E-value
SMN pfam06003
Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor ...
 26-259 5.19e-89

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.


Pssm-ID: 428716 [Multi-domain]  Cd Length: 264  Bit Score: 264.56  E-value: 5.19e-89
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQWKVGDKCSAIWS 103
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEWKVGDSCNAFWS 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027 104 EDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICEVANNIEQNAQENENESqvSTDESENS-RSPGNKSDN 182
Cdd:pfam06003  81 EDGNLYPATITSIDQKKGTCVVFYTGYGNEEEQNLADLLTPPPDMDEDALKTANVNETES--STDESDRSsGSAKHKSKS 158

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357027 183 --IKPKSAPWN-SFLPPPPPMPGPRLGPGKIIPPPPPI---------------------CPDSLDDADALGSMLISWYMS 238
Cdd:pfam06003 159 nfPMGPPSPWNpSFPPGPPPPPPGFGRHGEKPRTLGPFlsgwpppfplgppmipppppmSPDFGEDDEALGSMLIAWYMS 238

                         250       260
                  ....*....|....*....|....
gi 2217357027 239 GYHTGYYMGFRQNQKE---GRCSH 259
Cdd:pfam06003 239 GYHTGYYLGLKQGRMEaaaSKKSH 262
Tudor_SMN cd20398
Tudor domain found in survival motor neuron protein (SMN) and similar proteins; SMN, also ...
 92-147 2.73e-31

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.


Pssm-ID: 410469  Cd Length: 56  Bit Score: 110.05  E-value: 2.73e-31
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2217357027  92 WKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSPICE 147
Cdd:cd20398     1 WKVGDKCRAVYSEDGIIYEATIVSIDAERGTCVVRYTGYGNEEEQNLSDLLPPSGE 56
Tudor_SMN_SPF30-like cd21182
Tudor domain found in survival motor neuron protein (SMN), motor neuron-related-splicing ...
 95-144 1.25e-19

Tudor domain found in survival motor neuron protein (SMN), motor neuron-related-splicing factor 30 (SPF30), and similar proteins; This group contains SMN, SPF30, Tudor domain-containing protein 3 (TDRD3), DNA excision repair protein ERCC-6-like 2 (ERCC6L2), 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. 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. TDRD3 is a scaffolding protein that specifically recognizes and binds dimethylarginine-containing 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. Members of this group contain a single 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.


Pssm-ID: 410549  Cd Length: 50  Bit Score: 79.60  E-value: 1.25e-19
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2217357027  95 GDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLSP 144
Cdd:cd21182     1 GDKCLAPYSDDGKYYEATIEEITEESDTATVVFDGYGNSEEVPLSDLKPL 50
Tudor_SPF30 cd20399
Tudor domain found in survival of motor neuron-related-splicing factor 30 (SPF30) and similar ...
 92-141 4.81e-14

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.


Pssm-ID: 410470 [Multi-domain]  Cd Length: 55  Bit Score: 65.02  E-value: 4.81e-14
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2217357027  92 WKVGDKCSAIWSEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDL 141
Cdd:cd20399     1 WKVGDKCMAVWSEDGQYYEATIEEIS-EDGTCTVTFDGYGNTEVTPLSQL 49
SMN_C cd22852
C-terminal oligomerization domain of the Survival Motor Neuron family; The survival motor ...
 224-252 6.37e-13

C-terminal oligomerization domain of the Survival Motor Neuron family; The survival motor neuron (SMN) protein family includes metazoan SMN and fungal SMN-like protein 1 (SMN1). SMN forms the oligomeric core of a multiprotein complex, called the SMN complex, that functions in the assembly and biogenesis of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is expressed in all tissues of metazoan organisms, but is particularly expressed at high levels in motor neurons. Schizosaccharomyces pombe SMN1 is essential for viability and has been shown to interact with human SMN and Sm proteins. Loss of function mutations in the SMN gene of humans cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. While most eukaryotes have a single copy of the SMN gene, humans have two; the telomeric SMN1 gene is deleted or mutated in SMA patients, whereas the centromeric SMN2 gene is unaffected and can be present in multiple copies. SMN has three highly conserved domains: a short N-terminal region that is responsible for binding with high affinity to Gemin2; a central Tudor domain that recognizes symmetric dimethylarginine (sDMA) modifications in arginine/glycine rich regions of a number of proteins involved in RNA processing, including the Sm proteins; and a C-terminal domain called the YG-box that is primarily responsible for oligomerization. This model represents the C-terminal oligomerization domain of SMN family proteins.


Pssm-ID: 439368  Cd Length: 29  Bit Score: 61.32  E-value: 6.37e-13
                          10        20
                  ....*....|....*....|....*....
gi 2217357027 224 DADALGSMLISWYMSGYHTGYYMGFRQNQ 252
Cdd:cd22852     1 DDEALKNLLMSWYMAGYYTGYYQGLQQAQ 29
Tudor_TDRD3 cd20413
Tudor domain found in Tudor domain-containing protein 3 (TDRD3) and similar proteins; TDRD3 is ...
 92-145 8.03e-13

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.


Pssm-ID: 410484  Cd Length: 53  Bit Score: 61.59  E-value: 8.03e-13
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2217357027  92 WKVGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLLsPI 145
Cdd:cd20413     1 WKPGDECLAKYWEDNKFYRAEVTAVHPSGKTAVVKFMEYGNYEEVLLSDIK-PI 53
TUDOR smart00333
Tudor domain; Domain of unknown function present in several RNA-binding proteins. 10 copies in ...
 90-147 3.25e-12

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).


Pssm-ID: 197660  Cd Length: 57  Bit Score: 59.98  E-value: 3.25e-12
                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 2217357027   90 QQWKVGDKCSAIWsEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDLLSPICE 147
Cdd:smart00333   1 PTFKVGDKVAARW-EDGEWYRARIVKVD-GEQLYEVFFIDYGNEEVVPPSDLRQLPEE 56
SMN_N cd22851
N-terminal Gemin2-binding domain of the Survival Motor Neuron family; The survival motor ...
 29-59 1.22e-10

N-terminal Gemin2-binding domain of the Survival Motor Neuron family; The survival motor neuron (SMN) protein family includes metazoan SMN and fungal SMN-like protein 1 (SMN1). SMN forms the oligomeric core of a multiprotein complex, called the SMN complex, that functions in the assembly and biogenesis of small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome. It is expressed in all tissues of metazoan organisms, but is particularly expressed at high levels in motor neurons. Schizosaccharomyces pombe SMN1 is essential for viability and has been shown to interact with human SMN and Sm proteins. Loss of function mutations in the SMN gene of humans cause spinal muscular atrophy (SMA), a leading genetic cause of infant mortality. While most eukaryotes have a single copy of the SMN gene, humans have two; the telomeric SMN1 gene is deleted or mutated in SMA patients, whereas the centromeric SMN2 gene is unaffected and can be present in multiple copies. SMN has three highly conserved domains: a short N-terminal region that is responsible for binding with high affinity to Gemin2; a central Tudor domain that recognizes symmetric dimethylarginine (sDMA) modifications in arginine/glycine rich regions of a number of proteins involved in RNA processing, including the Sm proteins; and a C-terminal domain called the YG-box that is primarily responsible for oligomerization. This model represents the N-terminal Gemin2-binding domain of SMN family proteins.


Pssm-ID: 439367  Cd Length: 32  Bit Score: 55.17  E-value: 1.22e-10
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2217357027  29 DDSDIWDDTALIKAYDKAVASFKHALKNGDI 59
Cdd:cd22851     1 DDSDIWDDSALIKAWDEAVAEYKKYHSIRAK 31
Tudor_SF cd04508
Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally ...
 95-141 7.76e-06

Tudor domain superfamily; The Tudor domain is a conserved structural domain, originally identified in the Tudor protein of Drosophila, that adopts a beta-barrel-like core structure containing four short beta-strands followed by an alpha-helical region. It binds to proteins with dimethylated arginine or lysine residues, and may also bind methylated histone tails to facilitate protein-protein interactions. Tudor domain-containing proteins may mediate protein-protein interactions required for various DNA-templated biological processes, such as RNA metabolism, as well as histone modification and the DNA damage response. Members of this superfamily contain one or more copies of the Tudor domain.


Pssm-ID: 410449 [Multi-domain]  Cd Length: 47  Bit Score: 42.19  E-value: 7.76e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2217357027  95 GDKCSAIWSEDGCIYPATIASIDFKReTCVVVYTgYGNREEQNLSDL 141
Cdd:cd04508     1 GDRVEAKWSDDGQWYPATVVAVNDDG-KYTVLFD-DGNEEEVSEDDI 45
Tudor_ERCC6L2 cd20400
Tudor domain found in DNA excision repair protein ERCC-6-like 2 (ERCC6L2) and similar proteins; ...
 92-135 4.37e-05

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.


Pssm-ID: 410471  Cd Length: 59  Bit Score: 40.39  E-value: 4.37e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 2217357027  92 WKVGDKCSAIWSEDGCIYPATIASIDFK---RETCVVVYTGYGNREE 135
Cdd:cd20400     1 WHVGDRCLAPYSGDGKLYEAVIKSISTDengKSFAVVKFLGYESDED 47
Tudor_TDRD1_rpt2 cd20409
second Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 93-141 2.14e-04

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.


Pssm-ID: 410480  Cd Length: 82  Bit Score: 38.98  E-value: 2.14e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2217357027  93 KVGDKCSAIWSEDGCIYPATIasIDFKRETCVVV-YTGYGNREEQNLSDL 141
Cdd:cd20409    27 AVGEVCCAQFTEDNQWYRASV--LAYSSEDSVLVgYIDFGNSEEVALSRL 74
Tudor_TDRD1_rpt1 cd20408
first Tudor domain found in Tudor domain-containing protein 1 (TDRD1) and similar proteins; ...
 94-142 7.46e-04

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.


Pssm-ID: 410479  Cd Length: 130  Bit Score: 38.50  E-value: 7.46e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 2217357027  94 VGDKCSAIWSEDGCIYPATIASIDFKRETCVVVYTGYGNREEQNLSDLL 142
Cdd:cd20408    49 VGEVCVAKYSEDQNWYRALVQTVDVQQKKAGVFYIDYGNEETVPLNRIQ 97
Tudor_ZGPAT cd20384
Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and ...
 93-142 2.92e-03

Tudor domain found in zinc finger CCCH-type with G patch domain-containing protein (ZGPAT) and similar proteins; ZGPAT, also called ZIP, G patch domain-containing protein 6 (GPATC6), GPATCH6, zinc finger CCCH domain-containing protein 9 (ZC3HDC9), ZC3H9, or zinc finger and G patch domain-containing protein, is a transcription repressor that specifically binds the 5'-GGAG[GA]A[GA]A-3' consensus sequence. It represses transcription by recruiting the chromatin multiprotein complex NuRD to target promoters. 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.


Pssm-ID: 410455  Cd Length: 55  Bit Score: 35.28  E-value: 2.92e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|
gi 2217357027  93 KVGDKCSAIWsEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDLL 142
Cdd:cd20384     6 KEGSRCLAKY-DDGLWYPATVTDID-EDGKYTVKFDSYGEVAVVELDDIL 53
Tudor_TDRD8 cd20430
Tudor domain found in Tudor domain-containing protein 8 (TDRD8) and similar proteins; TDRD8, ...
 100-141 6.74e-03

Tudor domain found in Tudor domain-containing protein 8 (TDRD8) and similar proteins; TDRD8, also called serine/threonine-protein kinase (EC 2.7.11.1) 31 (STK31), serine/threonine-protein kinase NYD-SPK, or Sugen kinase 396 (SgK396), is a germ cell-specific factor expressed in embryonic gonocytes of both sexes, and in postnatal spermatocytes and round spermatids in males. It acts as a cell-cycle regulated protein that contributes to the tumorigenicity of epithelial cancer cells. TDRD8 contains a Tudor domain and a serine/threonine kinase 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.


Pssm-ID: 410501 [Multi-domain]  Cd Length: 75  Bit Score: 34.57  E-value: 6.74e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2217357027 100 AIWSEDGCIYPATIASIDfKRETCVVVYTGYGNREEQNLSDL 141
Cdd:cd20430    27 GKFSEDNCWYRCKVKSIL-SDEKCTVQYIDYGNTETVSRSSI 67
Tudor_TDRD11 cd20433
Tudor domain found in Tudor domain-containing protein 11 (TDRD11) and similar proteins; TDRD11, ...
 93-135 7.64e-03

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.


Pssm-ID: 410504 [Multi-domain]  Cd Length: 84  Bit Score: 34.58  E-value: 7.64e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2217357027  93 KVGDKCSAIWSEDGCIYPATIASIDfKRETCVVVYTGYGNREE 135
Cdd:cd20433    29 RKGDLCAAKFVEDGEWYRAKVEKVE-GDKKVHVLYIDYGNREV 70
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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