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Conserved domains on  [gi|62988868|gb|AAY24255|]
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unknown [Homo sapiens]

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 pfam06372
Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian ...
 1-86 3.11e-50

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: 156.27  E-value: 3.11e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62988868     1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVRE 80
Cdd:pfam06372   1 MSEWMKKSPLEWTDYTYKEVRVLASENREYKGWVLTTDPVSANIVLVNFLEDGAWSVTGIMGHAVQTVETQQEGDHRVRE 80


                  ....*.
gi 62988868    81 KLMHLF 86
Cdd:pfam06372  81 KLMHPF 86
Gemin6_C pfam20417
Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus ...
 88-167 5.89e-47

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: 147.52  E-value: 5.89e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62988868    88 SGDCKAYSPEDLEERKNSLKKWLEKNHIPITEQGDAPRTLCVAGVLTIDPPYGPENCSSSNEIILSRVQDLIEGHLTASQ 167
Cdd:pfam20417   1 QGDAKGHSPEDLEEKKSNLKKWLEKNHIPVTEEGDADELLCVAGVLCIDPPYAPENCRSSNEIILQRIQDLIQGHLSAEE 80
 
Name Accession Description Interval E-value
Gemin6 pfam06372
Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian ...
 1-86 3.11e-50

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: 156.27  E-value: 3.11e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62988868     1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVRE 80
Cdd:pfam06372   1 MSEWMKKSPLEWTDYTYKEVRVLASENREYKGWVLTTDPVSANIVLVNFLEDGAWSVTGIMGHAVQTVETQQEGDHRVRE 80


                  ....*.
gi 62988868    81 KLMHLF 86
Cdd:pfam06372  81 KLMHPF 86
Gemin6_C pfam20417
Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus ...
 88-167 5.89e-47

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: 147.52  E-value: 5.89e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62988868    88 SGDCKAYSPEDLEERKNSLKKWLEKNHIPITEQGDAPRTLCVAGVLTIDPPYGPENCSSSNEIILSRVQDLIEGHLTASQ 167
Cdd:pfam20417   1 QGDAKGHSPEDLEEKKSNLKKWLEKNHIPVTEEGDADELLCVAGVLCIDPPYAPENCRSSNEIILQRIQDLIQGHLSAEE 80
Gemin6 cd11676
Gemin 6; Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and ...
 9-71 8.73e-32

Gemin 6; Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 6 forms a heterodimer with Gemin 7, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring.


Pssm-ID: 212487  Cd Length: 63  Bit Score: 108.50  E-value: 8.73e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62988868   9 PLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETM 71
Cdd:cd11676   1 PLEWKSYVGKEVKVTASDGKTYTGWVYTVDPVSASVVLVQFLEDEKDKVKVVMGHAVKSVEVV 63
 
Name Accession Description Interval E-value
Gemin6 pfam06372
Gemin6 Sm-like domain; This entry represents the N-terminal Sm-like domain from mammalian ...
 1-86 3.11e-50

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: 156.27  E-value: 3.11e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62988868     1 MSEWMKKGPLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETMNEGDHRVRE 80
Cdd:pfam06372   1 MSEWMKKSPLEWTDYTYKEVRVLASENREYKGWVLTTDPVSANIVLVNFLEDGAWSVTGIMGHAVQTVETQQEGDHRVRE 80


                  ....*.
gi 62988868    81 KLMHLF 86
Cdd:pfam06372  81 KLMHPF 86
Gemin6_C pfam20417
Gemin6 C-terminal domain; This entry corresponds to a putative domain found at the C-terminus ...
 88-167 5.89e-47

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: 147.52  E-value: 5.89e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 62988868    88 SGDCKAYSPEDLEERKNSLKKWLEKNHIPITEQGDAPRTLCVAGVLTIDPPYGPENCSSSNEIILSRVQDLIEGHLTASQ 167
Cdd:pfam20417   1 QGDAKGHSPEDLEEKKSNLKKWLEKNHIPVTEEGDADELLCVAGVLCIDPPYAPENCRSSNEIILQRIQDLIQGHLSAEE 80
Gemin6 cd11676
Gemin 6; Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and ...
 9-71 8.73e-32

Gemin 6; Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 6 forms a heterodimer with Gemin 7, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring.


Pssm-ID: 212487  Cd Length: 63  Bit Score: 108.50  E-value: 8.73e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 62988868   9 PLEWQDYIYKEVRVTASEKNEYKGWVLTTDPVSANIVLVNFLEDGSMSVTGIMGHAVQTVETM 71
Cdd:cd11676   1 PLEWKSYVGKEVKVTASDGKTYTGWVYTVDPVSASVVLVQFLEDEKDKVKVVMGHAVKSVEVV 63
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 12-69 9.24e-06

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: 41.47  E-value: 9.24e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 62988868  12 WQDYIYKEVRVTASEKNEYKGWVLTTDPvSANIVLVNFLE------DGSMSVTGIMGHAVQTVE 69
Cdd:cd00600   1 LKDFIGKTVSVELKDGRVLTGTLVAFDK-YMNLVLDDVVEtgrdgkVRVLGLVLIRGSNIVSIR 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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