LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 7706423     13 LDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPddqyklteDTRQLGLVVCRGTSVVLICP 86
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDG--------EVRKLGLVLIRGNNIVLISP 66

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7706423   15 LSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDpddqykltEDTRQLGLVVCRGTSVVLI 84
Cdd:COG1958   9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDG--------EVVRKLGTVVIRGDNVVFI 70

LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.

                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 7706423     13 LDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPddqyklteDTRQLGLVVCRGTSVVLICP 86
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDG--------EVRKLGLVLIRGNNIVLISP 66

Sm protein G; 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 G binds subunits E and F 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        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 7706423   14 DLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDpddqyklTEDTRqLGLVVCRGTSVVLICPQD 88
Cdd:cd01719   4 ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGD-------GEKTP-IGMVVIRGNSIIMIEALD 70

archaeal Sm protein 1; The archaeal Sm1 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        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 7706423   15 LSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDpddqykltEDTRQLGLVVCRGTSVVLICP 86
Cdd:cd01731   6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEG--------ESVRKLGTVLVRGDNVVFISP 69

small nuclear ribonucleoprotein; Provisional

                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 7706423    13 LD-LSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTiEYMRDpddqyklTEDTRQLGLVVCRGTSVVLICP 86
Cdd:PRK00737   6 LDvLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNA-EEIQD-------GEVVRKLGKVVIRGDNVVYVSP 72

LSM domain containing 1; 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. LSMD1 proteins have a single Sm-like domain structure. Sm-like proteins exist in archaea as well as prokaryotes, forming heptameric and hexameric ring structures similar to those found in eukaryotes.

                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 7706423   12 ILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMRDPDdqyKLTEDTRQLGLVV 75
Cdd:cd06168   1 RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD---LGAEEPRSLGLVM 61

Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. 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 7706423   12 ILDLSKYIDKTIRVKFQGGREASGILKGFDPLLNLVLDGTIEYMrDPDDQYKLTEdtrqLGLVVCRGTSVVLIC 85
Cdd:cd01728   4 TASLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERI-IVGNQYGDIP----RGLFIIRGENVVLLG 72

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 7706423   17 KYIDKTIRVKFQG-GREASGILKGFDPLLNLVLDGTIEYMRDpddqykltEDTRQLGLVVCRGTSVVLICP 86
Cdd:cd11678   7 SLVGSRIRVEMKGdENQLQGRLVAVDDYMNLHLTDTMECVGE--------EKVRSLGTVVLRGNNILLIQP 69

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 7706423   14 DLSKYIDKTIRVKFQGGREASGILKGFDPL-LNLVL 48
Cdd:cd11679   4 ELNSLLDKEVIVTLSNGKTYTGQLVGFDPSsLNIVL 39

small nuclear ribonucleoprotein; Provisional

                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 7706423    35 GILKGFDPLLNLVLDGTIEYmrdpddqYKLTEDTRQLGLVVCRGTSVVLIC 85
Cdd:PTZ00138  43 GKILGFDEYMNMVLDDAEEV-------YTKKNTRKDLGRILLKGDNITLIM 86

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 7706423   35 GILKGFDPLLNLVLDGTIEYmrdpddqYKLTEDTRQLGLVVCRGTSVVLICP 86
Cdd:cd01718  35 GKIIGFDEYMNLVLDDAEEV-------HLKTNTRKPLGRILLKGDNITLIQN 79