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Conserved domains on  [gi|672082702|ref|XP_008770165|]
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small nuclear ribonucleoprotein Sm D1 isoform X1 [Rattus norvegicus]

Protein Classification

LSm family protein( domain architecture ID 249)

LSm family protein such as eukaryotic LSm (Sm-like proteins) and bacterial LSm-related Hfq proteins, that have an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and are involved in processes associated with RNA processing and gene expression regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 2-52 8.29e-20

Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


The actual alignment was detected with superfamily member cd01724:

Pssm-ID: 469694  Cd Length: 92  Bit Score: 75.34  E-value: 8.29e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672082702  2 KLVRFLMKLSHETVTIELKNGTQVHGTIT-----------------------------------------DSLPLDTLLV 40
Cdd:cd01724   1 KLVRFLMKLSNETVTIELKNGTVVHGTITgvdvsmnthlknvkltlkgknpvsldtlsirgnniryiilpDSLNLDTLLV 80

                        90
                ....*....|..
gi 672082702 41 DVEPKVKSKKRE 52
Cdd:cd01724  81 DDTPKAKAKKRA 92
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-52 8.29e-20

Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 75.34  E-value: 8.29e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672082702  2 KLVRFLMKLSHETVTIELKNGTQVHGTIT-----------------------------------------DSLPLDTLLV 40
Cdd:cd01724   1 KLVRFLMKLSNETVTIELKNGTVVHGTITgvdvsmnthlknvkltlkgknpvsldtlsirgnniryiilpDSLNLDTLLV 80

                        90
                ....*....|..
gi 672082702 41 DVEPKVKSKKRE 52
Cdd:cd01724  81 DDTPKAKAKKRA 92
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-30 3.97e-03

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 32.47  E-value: 3.97e-03
                          10        20
                  ....*....|....*....|....*.
gi 672082702    5 RFLMKLSHETVTIELKNGTQVHGTIT 30
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLK 26
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-52 8.29e-20

Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 75.34  E-value: 8.29e-20
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 672082702  2 KLVRFLMKLSHETVTIELKNGTQVHGTIT-----------------------------------------DSLPLDTLLV 40
Cdd:cd01724   1 KLVRFLMKLSNETVTIELKNGTVVHGTITgvdvsmnthlknvkltlkgknpvsldtlsirgnniryiilpDSLNLDTLLV 80

                        90
                ....*....|..
gi 672082702 41 DVEPKVKSKKRE 52
Cdd:cd01724  81 DDTPKAKAKKRA 92
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-30 3.97e-03

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 32.47  E-value: 3.97e-03
                          10        20
                  ....*....|....*....|....*.
gi 672082702    5 RFLMKLSHETVTIELKNGTQVHGTIT 30
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLK 26
 
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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