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Conserved domains on  [gi|2048774995|ref|NP_001382066|]
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gem-associated protein 6 isoform 2 [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
Gemin6_C pfam20417
Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus ...
 28-107 1.66e-49

Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus of several mammalian Gemin6 proteins. This domain appears to be distantly related to pfam09793 suggesting it may have an RNA-binding function. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.


:

Pssm-ID: 466566  Cd Length: 80  Bit Score: 151.76  E-value: 1.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774995  28 SADCKGYSPEDLEKKKTSLKKWLEKNHIPVTEEGDTQRTLCVAGVLTIDPPYAPENCSSSNEIILSRIQDLIQGHLSASQ 107
Cdd:pfam20417   1 QGDAKGHSPEDLEEKKSNLKKWLEKNHIPVTEEGDADELLCVAGVLCIDPPYAPENCRSSNEIILQRIQDLIQGHLSAEE 80
Gemin6 super family cl47948
Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian ...
 1-26 1.59e-09

Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.


The actual alignment was detected with superfamily member pfam06372:

Pssm-ID: 461887  Cd Length: 86  Bit Score: 50.34  E-value: 1.59e-09
                          10        20
                  ....*....|....*....|....*.
gi 2048774995   1 MGHSVQTVETVSEGDHRVREKLMHLF 26
Cdd:pfam06372  61 MGHAVQTVETQQEGDHRVREKLMHPF 86
 
Name Accession Description Interval E-value
Gemin6_C pfam20417
Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus ...
 28-107 1.66e-49

Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus of several mammalian Gemin6 proteins. This domain appears to be distantly related to pfam09793 suggesting it may have an RNA-binding function. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.


Pssm-ID: 466566  Cd Length: 80  Bit Score: 151.76  E-value: 1.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774995  28 SADCKGYSPEDLEKKKTSLKKWLEKNHIPVTEEGDTQRTLCVAGVLTIDPPYAPENCSSSNEIILSRIQDLIQGHLSASQ 107
Cdd:pfam20417   1 QGDAKGHSPEDLEEKKSNLKKWLEKNHIPVTEEGDADELLCVAGVLCIDPPYAPENCRSSNEIILQRIQDLIQGHLSAEE 80
Gemin6 pfam06372
Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian ...
 1-26 1.59e-09

Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.


Pssm-ID: 461887  Cd Length: 86  Bit Score: 50.34  E-value: 1.59e-09
                          10        20
                  ....*....|....*....|....*.
gi 2048774995   1 MGHSVQTVETVSEGDHRVREKLMHLF 26
Cdd:pfam06372  61 MGHAVQTVETQQEGDHRVREKLMHPF 86
 
Name Accession Description Interval E-value
Gemin6_C pfam20417
Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus ...
 28-107 1.66e-49

Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus of several mammalian Gemin6 proteins. This domain appears to be distantly related to pfam09793 suggesting it may have an RNA-binding function. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.


Pssm-ID: 466566  Cd Length: 80  Bit Score: 151.76  E-value: 1.66e-49
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2048774995  28 SADCKGYSPEDLEKKKTSLKKWLEKNHIPVTEEGDTQRTLCVAGVLTIDPPYAPENCSSSNEIILSRIQDLIQGHLSASQ 107
Cdd:pfam20417   1 QGDAKGHSPEDLEEKKSNLKKWLEKNHIPVTEEGDADELLCVAGVLCIDPPYAPENCRSSNEIILQRIQDLIQGHLSAEE 80
Gemin6 pfam06372
Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian ...
 1-26 1.59e-09

Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian Gemin6 proteins. The exact function of Gemin6 is unknown but it has been found to form part of the pfam06003 complex. The SMN complex plays a key role in the biogenesis of spliceosomal small nuclear ribonucleoproteins (snRNPs) and other ribonucleoprotein particles.


Pssm-ID: 461887  Cd Length: 86  Bit Score: 50.34  E-value: 1.59e-09
                          10        20
                  ....*....|....*....|....*.
gi 2048774995   1 MGHSVQTVETVSEGDHRVREKLMHLF 26
Cdd:pfam06372  61 MGHAVQTVETQQEGDHRVREKLMHPF 86
 
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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