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.

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                 ....*....|....*....|....*....|....*
gi 2022781935  9 PFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQ 43
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLV 35

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

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                 ....*....|....*....|....*....|..
gi 2022781935 11 LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNM 42
Cdd:COG1958    9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNL 40

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
                 ....*....|....*....|....*....|....*.
gi 2022781935  6 NPKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMN 41
Cdd:cd01726    1 TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMN 36

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

                          10        20        30
                  ....*....|....*....|....*....|....*
gi 2022781935   9 PFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQ 43
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLV 35

Like-Sm protein 4; 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
                 ....*....|....*....|....*....|....*....|
gi 2022781935  3 LPLNpkpFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNM 42
Cdd:cd01723    1 LPLS---LLRTAQGHPVLVELKNGETYNGHLVNCDNWMNI 37

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.

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                 ....*....|....*....|....*....|..
gi 2022781935 11 LNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNM 42
Cdd:cd01731    6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNL 37

Like-Sm protein 2; 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
                 ....*....|....*....|....*....|...
gi 2022781935 10 FLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNM 42
Cdd:cd01725    5 FFKTLVGKEVTVELKNDLSITGTLHSVDQYLNI 37

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
                 ....*....|....*....|....*..
gi 2022781935 11 LNGLTGKPVMVKLKWGMEYKGYLVSVD 37
Cdd:cd11679    5 LNSLLDKEVIVTLSNGKTYTGQLVGFD 31