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Conserved domains on  [gi|2217357039|ref|XP_047273577|]
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survival motor neuron protein isoform X6 [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 ...
 26-211 8.41e-38

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: 132.43  E-value: 8.41e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQ------------ 91
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEwkvgdscnafws 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039  92 -----------------------------------------------------NENESQVSTDESENS-RSPGNKSDN-- 115
Cdd:pfam06003  81 edgnlypatitsidqkkgtcvvfytgygneeeqnladlltpppdmdedalktaNVNETESSTDESDRSsGSAKHKSKSnf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039 116 IKPKSAPWNsflppppPMPGPRLGPGKPGLKFNGPPPPPPPPpphLLSCWLPPFPSGPPIIPPPPPICPDSLDDADALGS 195
Cdd:pfam06003 161 PMGPPSPWN-------PSFPPGPPPPPPGFGRHGEKPRTLGP---FLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEALGS 230

                         250
                  ....*....|....*.
gi 2217357039 196 MLISWYMSGYHTGYYM 211
Cdd:pfam06003 231 MLIAWYMSGYHTGYYL 246
 
Name Accession Description Interval E-value
SMN pfam06003
Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor ...
 26-211 8.41e-38

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: 132.43  E-value: 8.41e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQ------------ 91
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEwkvgdscnafws 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039  92 -----------------------------------------------------NENESQVSTDESENS-RSPGNKSDN-- 115
Cdd:pfam06003  81 edgnlypatitsidqkkgtcvvfytgygneeeqnladlltpppdmdedalktaNVNETESSTDESDRSsGSAKHKSKSnf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039 116 IKPKSAPWNsflppppPMPGPRLGPGKPGLKFNGPPPPPPPPpphLLSCWLPPFPSGPPIIPPPPPICPDSLDDADALGS 195
Cdd:pfam06003 161 PMGPPSPWN-------PSFPPGPPPPPPGFGRHGEKPRTLGP---FLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEALGS 230

                         250
                  ....*....|....*.
gi 2217357039 196 MLISWYMSGYHTGYYM 211
Cdd:pfam06003 231 MLIAWYMSGYHTGYYL 246
SMN_N cd22851
N-terminal Gemin2-binding domain of the Survival Motor Neuron family; The survival motor ...
 29-59 5.29e-11

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: 55.55  E-value: 5.29e-11
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2217357039  29 DDSDIWDDTALIKAYDKAVASFKHALKNGDI 59
Cdd:cd22851     1 DDSDIWDDSALIKAWDEAVAEYKKYHSIRAK 31
 
Name Accession Description Interval E-value
SMN pfam06003
Survival motor neuron protein (SMN); This family consists of several eukaryotic survival motor ...
 26-211 8.41e-38

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: 132.43  E-value: 8.41e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039  26 GQSDDSDIWDDTALIKAYDKAVASFKHALKNGDICETSGKPKTTP--KRKPAKKNKSQKKNTAASLQQ------------ 91
Cdd:pfam06003   1 GQSDDSDIWDDTALIKAYDKAVASFKNALKNGDCATPQENDEQNPgkKRKNNKKNRSRKKCNAAPLKEwkvgdscnafws 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039  92 -----------------------------------------------------NENESQVSTDESENS-RSPGNKSDN-- 115
Cdd:pfam06003  81 edgnlypatitsidqkkgtcvvfytgygneeeqnladlltpppdmdedalktaNVNETESSTDESDRSsGSAKHKSKSnf 160

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217357039 116 IKPKSAPWNsflppppPMPGPRLGPGKPGLKFNGPPPPPPPPpphLLSCWLPPFPSGPPIIPPPPPICPDSLDDADALGS 195
Cdd:pfam06003 161 PMGPPSPWN-------PSFPPGPPPPPPGFGRHGEKPRTLGP---FLSGWPPPFPLGPPMIPPPPPMSPDFGEDDEALGS 230

                         250
                  ....*....|....*.
gi 2217357039 196 MLISWYMSGYHTGYYM 211
Cdd:pfam06003 231 MLIAWYMSGYHTGYYL 246
SMN_N cd22851
N-terminal Gemin2-binding domain of the Survival Motor Neuron family; The survival motor ...
 29-59 5.29e-11

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: 55.55  E-value: 5.29e-11
                          10        20        30
                  ....*....|....*....|....*....|.
gi 2217357039  29 DDSDIWDDTALIKAYDKAVASFKHALKNGDI 59
Cdd:cd22851     1 DDSDIWDDSALIKAWDEAVAEYKKYHSIRAK 31
SMN_C cd22852
C-terminal oligomerization domain of the Survival Motor Neuron family; The survival motor ...
 189-211 7.76e-10

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: 52.46  E-value: 7.76e-10
                          10        20
                  ....*....|....*....|...
gi 2217357039 189 DADALGSMLISWYMSGYHTGYYM 211
Cdd:cd22852     1 DDEALKNLLMSWYMAGYYTGYYQ 23
 
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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