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Conserved domains on  [gi|1610576122|ref|NP_001356415|]
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protein LSM12 isoform 4 [Homo sapiens]

Protein Classification

LSm family protein( domain architecture ID 10216552)

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 ...
 28-107 2.02e-32

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: 109.70  E-value: 2.02e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1610576122   28 ELASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCK--GKEGSALSHVR 105
Cdd:smart00995   9 RVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEVTISPPYTVENVKklSGNSKALERVQ 88


                   ..
gi 1610576122  106 KI 107
Cdd:smart00995  89 KI 90
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 7-28 1.82e-08

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 cd01735:

Pssm-ID: 469694  Cd Length: 61  Bit Score: 47.74  E-value: 1.82e-08
                          10        20
                  ....*....|....*....|..
gi 1610576122   7 EYFSVGSQVSCRTCQEQRLQGE 28
Cdd:cd01735     1 EYFSVGSQVSCKTCFGQRIQGE 22
 
Name Accession Description Interval E-value
AD smart00995
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 28-107 2.02e-32

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: 109.70  E-value: 2.02e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1610576122   28 ELASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCK--GKEGSALSHVR 105
Cdd:smart00995   9 RVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEVTISPPYTVENVKklSGNSKALERVQ 88


                   ..
gi 1610576122  106 KI 107
Cdd:smart00995  89 KI 90
AD pfam09793
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 29-107 2.09e-26

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: 94.58  E-value: 2.09e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1610576122  29 LASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGS----ALSHV 104
Cdd:pfam09793   8 LQARLRKAIEEAKAKLARIGKGVSPEGQAIFDALSKTLPDVRWKGKNIVVLDEVIIAPPYKVENCKKLGSSgnpkALERV 87


                  ...
gi 1610576122 105 RKI 107
Cdd:pfam09793  88 KKI 90
LSm12_N cd01735
Like-Sm protein 12, N-terminal domain; LSm12 belongs to a family of Sm-like proteins that ...
 7-28 1.82e-08

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: 47.74  E-value: 1.82e-08
                          10        20
                  ....*....|....*....|..
gi 1610576122   7 EYFSVGSQVSCRTCQEQRLQGE 28
Cdd:cd01735     1 EYFSVGSQVSCKTCFGQRIQGE 22
 
Name Accession Description Interval E-value
AD smart00995
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 28-107 2.02e-32

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: 109.70  E-value: 2.02e-32
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1610576122   28 ELASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCK--GKEGSALSHVR 105
Cdd:smart00995   9 RVKKRLRKAIEQAKRKADSKGKGVSPEGQEIFDAIAKTIPDCRWQGKNIVVLDEVTISPPYTVENVKklSGNSKALERVQ 88


                   ..
gi 1610576122  106 KI 107
Cdd:smart00995  89 KI 90
AD pfam09793
Anticodon-binding domain; This domain of approximately 100 residues is conserved from plants ...
 29-107 2.09e-26

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: 94.58  E-value: 2.09e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1610576122  29 LASKARTEKEEKLSQAYAISAGVSLEGQQLFQTIHKTIKDCKWQEKNIVVMEEVVITPPYQVENCKGKEGS----ALSHV 104
Cdd:pfam09793   8 LQARLRKAIEEAKAKLARIGKGVSPEGQAIFDALSKTLPDVRWKGKNIVVLDEVIIAPPYKVENCKKLGSSgnpkALERV 87


                  ...
gi 1610576122 105 RKI 107
Cdd:pfam09793  88 KKI 90
LSm12_N cd01735
Like-Sm protein 12, N-terminal domain; LSm12 belongs to a family of Sm-like proteins that ...
 7-28 1.82e-08

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: 47.74  E-value: 1.82e-08
                          10        20
                  ....*....|....*....|..
gi 1610576122   7 EYFSVGSQVSCRTCQEQRLQGE 28
Cdd:cd01735     1 EYFSVGSQVSCKTCFGQRIQGE 22
 
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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