Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114158715   9 KESIFDLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDPDDQYKLTEDTRQLGLVVCRGTSVVLICPQD 88
Cdd:cd01729    1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSVVLISPVD 80

                 ....*....
gi 114158715  89 GMEAIPNPF 97
Cdd:cd01729   81 GTEEIENPF 89

Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114158715   9 KESIFDLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDPDDQYKLTEDTRQLGLVVCRGTSVVLICPQD 88
Cdd:cd01729    1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSVVLISPVD 80

                 ....*....
gi 114158715  89 GMEAIPNPF 97
Cdd:cd01729   81 GTEEIENPF 89

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 114158715    14 DLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDpddqyklTEDTRQLGLVVCRGTSVVLICP 86
Cdd:smart00651   2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------GEKKRKLGLVFIRGNNIVYIIL 67

small nuclear ribonucleoprotein; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 114158715  15 LSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTiEYMRDpddqyklTEDTRQLGLVVCRGTSVVLICP 86
Cdd:PRK00737   9 LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNA-EEIQD-------GEVVRKLGKVVIRGDNVVYVSP 72

Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114158715   9 KESIFDLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDPDDQYKLTEDTRQLGLVVCRGTSVVLICPQD 88
Cdd:cd01729    1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSVVLISPVD 80

                 ....*....
gi 114158715  89 GMEAIPNPF 97
Cdd:cd01729   81 GTEEIENPF 89

snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 114158715    14 DLSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDpddqyklTEDTRQLGLVVCRGTSVVLICP 86
Cdd:smart00651   2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKD-------GEKKRKLGLVFIRGNNIVYIIL 67

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114158715  15 LSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDpddqykltEDTRQLGLVVCRGTSVVLI 84
Cdd:COG1958    9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDG--------EVVRKLGTVVIRGDNVVFI 70

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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114158715  15 LSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYMRDPDDqykltedtRQLGLVVCRGTSVVLIC 85
Cdd:cd00600    1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKV--------RVLGLVLIRGSNIVSIR 63

Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 114158715  15 LSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYmRDPDDQYKLT----EDTRQLGLVVCRGTSVV 82
Cdd:cd01717    5 MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEF-RKIKPKKKKKgeerEEKRVLGLVLLRGENVV 75

Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. 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.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 114158715  13 FDLSKY-IDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYM----RDPDDQYKLTEDT-RQLGLVVCRGTSVVLICP 86
Cdd:cd01730    3 LDLIRLsLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETIttveIDEETYEEIYKTTkRNIPMLFVRGDGVILVSP 82

archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114158715  17 KYIDKHIRVKFQG-GREASGVLKGFDPLLNLVLDGTIEYMRDpddqykltEDTRQLGLVVCRGTSVVLICP 86
Cdd:cd11678    7 SLVGSRIRVEMKGdENQLQGRLVAVDDYMNLHLTDTMECVGE--------EKVRSLGTVVLRGNNILLIQP 69

Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus uridylation tag of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. LSm2-8 form the core of the snRNP particle that, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. LSm1-7 is involved in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm657 is believed to be an assembly intermediate for both the LSm1-7 and LSm2-8 rings. 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.

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 114158715  15 LSKYIDKHIRVKFQGGREASGVLKGFDPLLNLVLDGTIEYmrdpDDQykltEDTRQLGLVVCRGTSVVLIC 85
Cdd:cd01726    6 LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEY----VDG----QLVAKYGDAFIRGNNVLYIS 68

Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a hetero-heptameric ring around the Sm site of the 2,2,7-trimethyl guanosine (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs) forming the core of the snRNP particle. The snRNP particle, in turn, assembles with other components onto the pre-mRNA to form the spliceosome which is responsible for the excision of introns and the ligation of exons. 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 subunit E binds subunits F and G to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming a seven-membered ring structure.

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 114158715  35 GVLKGFDPLLNLVLDGTIEYmrdpddqYKLTEDTRQLGLVVCRGTSVVLICP 86
Cdd:cd01718   35 GKIIGFDEYMNLVLDDAEEV-------HLKTNTRKPLGRILLKGDNITLIQN 79

archaeal Sm-related protein; Archaeal Sm-related proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.

                         10        20        30
                 ....*....|....*....|....*....|....*.
gi 114158715  14 DLSKYIDKHIRVKFQGGREASGVLKGFDPL-LNLVL 48
Cdd:cd11679    4 ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSsLNIVL 39