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Conserved domains on  [gi|768016198|ref|XP_011526911|]
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protein LSM14 homolog B isoform X6 [Homo sapiens]

Protein Classification

LSM14 family protein( domain architecture ID 10109663)

LSM14 family protein having an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, may be involved in essential RNA-processing tasks

Gene Ontology:  GO:1990904|GO:0006417|GO:0003729
PubMed:  15225602|29510985|12438310

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LSm14_N cd01736
Like-Sm protein 14, N-terminal domain; LSm14 (also known as RAP55) belongs to a family of ...
 6-79 7.44e-45

Like-Sm protein 14, N-terminal domain; LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that 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, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.


:

Pssm-ID: 212483  Cd Length: 74  Bit Score: 149.66  E-value: 7.44e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 768016198   6 GTPYLGSKISLISKAQIRYEGILYTIDTDNSTVALAKVRSFGTEDRPTDRPAPPREEIYEYIIFRGSDIKDITV 79
Cdd:cd01736    1 GTPYIGSKISLISKSDIRYEGILYTIDTEDSTIALKNVRSFGTEGRPTGRPIPPSDEVYDYIVFRGSDIKDLTV 74
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 273-375 2.32e-26

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


:

Pssm-ID: 430668  Cd Length: 104  Bit Score: 101.76  E-value: 2.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768016198  273 IKFEGDFDFESANAQFNREELDKEFKKklnfkddKAEKGEEKDLAVVTQSAEAPAEEDLLGPNCYYDKSKSFFDNISSEL 352
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRK-------NDKLDEEKRLVNENNATRVATNEQPNEEVKGVYKKDDFFDNISSEA 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 768016198  353 KTSSRRT-------TWAEERKLNTETFGVS 375
Cdd:pfam09532  74 NDRGIQSgpspsgrDWREERSLNTETFGVD 103
 
Name Accession Description Interval E-value
LSm14_N cd01736
Like-Sm protein 14, N-terminal domain; LSm14 (also known as RAP55) belongs to a family of ...
 6-79 7.44e-45

Like-Sm protein 14, N-terminal domain; LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that 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, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.


Pssm-ID: 212483  Cd Length: 74  Bit Score: 149.66  E-value: 7.44e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 768016198   6 GTPYLGSKISLISKAQIRYEGILYTIDTDNSTVALAKVRSFGTEDRPTDRPAPPREEIYEYIIFRGSDIKDITV 79
Cdd:cd01736    1 GTPYIGSKISLISKSDIRYEGILYTIDTEDSTIALKNVRSFGTEGRPTGRPIPPSDEVYDYIVFRGSDIKDLTV 74
LSM14 pfam12701
Scd6-like Sm domain; The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from ...
 8-82 9.84e-42

Scd6-like Sm domain; The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans. The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain. In addition both EDC3 and Scd6p are found fused to the FDF domain.


Pssm-ID: 463675  Cd Length: 75  Bit Score: 141.49  E-value: 9.84e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768016198    8 PYLGSKISLISKAQIRYEGILYTIDTDNSTVALAKVRSFGTEDRPTDRPAPPREEIYEYIIFRGSDIKDITVCEP 82
Cdd:pfam12701   1 PFIGSRISLISKSDIRYEGILHSIDTEDSTITLKNVRSFGTEGRGPGPQEPPSDEVYEYIVFRGSDIKDLKILEP 75
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 273-375 2.32e-26

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


Pssm-ID: 430668  Cd Length: 104  Bit Score: 101.76  E-value: 2.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768016198  273 IKFEGDFDFESANAQFNREELDKEFKKklnfkddKAEKGEEKDLAVVTQSAEAPAEEDLLGPNCYYDKSKSFFDNISSEL 352
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRK-------NDKLDEEKRLVNENNATRVATNEQPNEEVKGVYKKDDFFDNISSEA 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 768016198  353 KTSSRRT-------TWAEERKLNTETFGVS 375
Cdd:pfam09532  74 NDRGIQSgpspsgrDWREERSLNTETFGVD 103
 
Name Accession Description Interval E-value
LSm14_N cd01736
Like-Sm protein 14, N-terminal domain; LSm14 (also known as RAP55) belongs to a family of ...
 6-79 7.44e-45

Like-Sm protein 14, N-terminal domain; LSm14 (also known as RAP55) belongs to a family of Sm-like proteins that 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, that associates with other Sm proteins to form hexameric and heptameric ring structures. In addition to the N-terminal Sm-like domain, LSm14 has an uncharacterized C-terminal domain containing a conserved DFDF box. In Xenopus laevis, LSm14 is an oocyte-specific constituent of ribonucleoprotein particles.


Pssm-ID: 212483  Cd Length: 74  Bit Score: 149.66  E-value: 7.44e-45
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 768016198   6 GTPYLGSKISLISKAQIRYEGILYTIDTDNSTVALAKVRSFGTEDRPTDRPAPPREEIYEYIIFRGSDIKDITV 79
Cdd:cd01736    1 GTPYIGSKISLISKSDIRYEGILYTIDTEDSTIALKNVRSFGTEGRPTGRPIPPSDEVYDYIVFRGSDIKDLTV 74
LSM14 pfam12701
Scd6-like Sm domain; The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from ...
 8-82 9.84e-42

Scd6-like Sm domain; The Scd6-like Sm domain is found in Scd6p from S. cerevisiae, Rap55 from the newt Pleurodeles walt, and its orthologs from fungi, animals, plants and apicomplexans. The domain is also found in Dcp3p and the human EDC3/FLJ21128 protein where it is fused to the the Rossmanoid YjeF-N domain. In addition both EDC3 and Scd6p are found fused to the FDF domain.


Pssm-ID: 463675  Cd Length: 75  Bit Score: 141.49  E-value: 9.84e-42
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 768016198    8 PYLGSKISLISKAQIRYEGILYTIDTDNSTVALAKVRSFGTEDRPTDRPAPPREEIYEYIIFRGSDIKDITVCEP 82
Cdd:pfam12701   1 PFIGSRISLISKSDIRYEGILHSIDTEDSTITLKNVRSFGTEGRGPGPQEPPSDEVYEYIVFRGSDIKDLKILEP 75
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 273-375 2.32e-26

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


Pssm-ID: 430668  Cd Length: 104  Bit Score: 101.76  E-value: 2.32e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768016198  273 IKFEGDFDFESANAQFNREELDKEFKKklnfkddKAEKGEEKDLAVVTQSAEAPAEEDLLGPNCYYDKSKSFFDNISSEL 352
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRK-------NDKLDEEKRLVNENNATRVATNEQPNEEVKGVYKKDDFFDNISSEA 73

                          90       100       110
                  ....*....|....*....|....*....|
gi 768016198  353 KTSSRRT-------TWAEERKLNTETFGVS 375
Cdd:pfam09532  74 NDRGIQSgpspsgrDWREERSLNTETFGVD 103
SM-ATX pfam14438
Ataxin 2 SM domain; This SM domain is found in Ataxin-2.
 11-79 6.80e-10

Ataxin 2 SM domain; This SM domain is found in Ataxin-2.


Pssm-ID: 464173  Cd Length: 78  Bit Score: 55.25  E-value: 6.80e-10
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768016198   11 GSKISLISKAQIRYEGILYTIDTDN-STVALAKVRSFGTEDRptDRPAPPREEIYEYIIFRGSDIKDITV 79
Cdd:pfam14438  10 GLVVEVTTKNGEVYEGIFSTASLEKdFGVVLKMARRIKKSNG--SGLNPVRGEIVDTMIFPAKDIVDIEA 77
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 9-78 1.43e-04

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.


Pssm-ID: 212462 [Multi-domain]  Cd Length: 63  Bit Score: 39.54  E-value: 1.43e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 768016198   9 YLGSKISLISKAQIRYEGILYTIDtDNSTVALAKVRSFGTEDRPTDrpappreeiYEYIIFRGSDIKDIT 78
Cdd:cd00600    4 FIGKTVSVELKDGRVLTGTLVAFD-KYMNLVLDDVVETGRDGKVRV---------LGLVLIRGSNIVSIR 63
 
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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