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Conserved domains on  [gi|47551343|ref|NP_999982|]
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protein LSM12 homolog B [Danio rerio]

Protein Classification

LSm family protein( domain architecture ID 10109624)

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
AD smart00995
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 79-166 1.19e-34

Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins.


:

Pssm-ID: 214962  Cd Length: 90  Bit Score: 117.79  E-value: 1.19e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47551343     79 PLASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIHKTIKECKWQEKNIIVMDDVVISPPYQVDNCK--GKE 156
Cdd:smart00995   1 PPAPVNLERVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEVTISPPYTVENVKklSGN 80

                           90
                   ....*....|
gi 47551343    157 GSALSHVRKI 166
Cdd:smart00995  81 SKALERVQKI 90
LSm12_N cd01735
Like-Sm protein 12, N-terminal domain; LSm12 belongs to a family of Sm-like proteins that ...
 8-68 6.86e-32

Like-Sm protein 12, N-terminal domain; LSm12 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, LSm12 has a novel methyltransferase domain.


:

Pssm-ID: 212482  Cd Length: 61  Bit Score: 109.76  E-value: 6.86e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47551343   8 EYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCAPSSGKPNLSDVMLVNLAYVSEVD 68
Cdd:cd01735   1 EYFSVGSQVSCKTCFGQRIQGEVVAFDHPSKMLALKCPSSSGKPNLADISIVNLDYVSDVE 61
 
Name Accession Description Interval E-value
AD smart00995
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 79-166 1.19e-34

Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins.


Pssm-ID: 214962  Cd Length: 90  Bit Score: 117.79  E-value: 1.19e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47551343     79 PLASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIHKTIKECKWQEKNIIVMDDVVISPPYQVDNCK--GKE 156
Cdd:smart00995   1 PPAPVNLERVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEVTISPPYTVENVKklSGN 80

                           90
                   ....*....|
gi 47551343    157 GSALSHVRKI 166
Cdd:smart00995  81 SKALERVQKI 90
LSm12_N cd01735
Like-Sm protein 12, N-terminal domain; LSm12 belongs to a family of Sm-like proteins that ...
 8-68 6.86e-32

Like-Sm protein 12, N-terminal domain; LSm12 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, LSm12 has a novel methyltransferase domain.


Pssm-ID: 212482  Cd Length: 61  Bit Score: 109.76  E-value: 6.86e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47551343   8 EYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCAPSSGKPNLSDVMLVNLAYVSEVD 68
Cdd:cd01735   1 EYFSVGSQVSCKTCFGQRIQGEVVAFDHPSKMLALKCPSSSGKPNLADISIVNLDYVSDVE 61
AD pfam09793
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 81-166 6.36e-31

Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. It is an anticodon-binding domain of a prolyl-tRNA synthetase, whose PDB structure is available under the identifier 1h4q.


Pssm-ID: 462905  Cd Length: 90  Bit Score: 108.06  E-value: 6.36e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47551343    81 ASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIHKTIKECKWQEKNIIVMDDVVISPPYQVDNCKGKEGS-- 158
Cdd:pfam09793   1 PPVDLNRLQARLRKAIEEAKAKLARIGKGVSPEGQAIFDALSKTLPDVRWKGKNIVVLDEVIIAPPYKVENCKKLGSSgn 80

                          90
                  ....*....|
gi 47551343   159 --ALSHVRKI 166
Cdd:pfam09793  81 pkALERVKKI 90
 
Name Accession Description Interval E-value
AD smart00995
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 79-166 1.19e-34

Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins.


Pssm-ID: 214962  Cd Length: 90  Bit Score: 117.79  E-value: 1.19e-34
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47551343     79 PLASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIHKTIKECKWQEKNIIVMDDVVISPPYQVDNCK--GKE 156
Cdd:smart00995   1 PPAPVNLERVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEVTISPPYTVENVKklSGN 80

                           90
                   ....*....|
gi 47551343    157 GSALSHVRKI 166
Cdd:smart00995  81 SKALERVQKI 90
LSm12_N cd01735
Like-Sm protein 12, N-terminal domain; LSm12 belongs to a family of Sm-like proteins that ...
 8-68 6.86e-32

Like-Sm protein 12, N-terminal domain; LSm12 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, LSm12 has a novel methyltransferase domain.


Pssm-ID: 212482  Cd Length: 61  Bit Score: 109.76  E-value: 6.86e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 47551343   8 EYFSVGSHVSCLTCLGQRLQGEVVAFDYPSKMLTLKCAPSSGKPNLSDVMLVNLAYVSEVD 68
Cdd:cd01735   1 EYFSVGSQVSCKTCFGQRIQGEVVAFDHPSKMLALKCPSSSGKPNLADISIVNLDYVSDVE 61
AD pfam09793
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 81-166 6.36e-31

Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants to humans. It is frequently found in association with Lsm domain-containing proteins. It is an anticodon-binding domain of a prolyl-tRNA synthetase, whose PDB structure is available under the identifier 1h4q.


Pssm-ID: 462905  Cd Length: 90  Bit Score: 108.06  E-value: 6.36e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 47551343    81 ASLNFNKLVNRARAEKEDKLSLAYAVSAGVSVEGQQLFQTIHKTIKECKWQEKNIIVMDDVVISPPYQVDNCKGKEGS-- 158
Cdd:pfam09793   1 PPVDLNRLQARLRKAIEEAKAKLARIGKGVSPEGQAIFDALSKTLPDVRWKGKNIVVLDEVIIAPPYKVENCKKLGSSgn 80

                          90
                  ....*....|
gi 47551343   159 --ALSHVRKI 166
Cdd:pfam09793  81 pkALERVKKI 90
 
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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