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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEervpktqldklrprkdskdgttLNIKVEKRVLGLTILRGEQ 91
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEE----------------------TIKDGEVRKLGLVLIRGNN 60

                  ...
gi 2078830397  92 ILS 94
Cdd:pfam01423  61 IVL 63

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEErvpktqldklrprkdsKDGTTlnikveKRVLGLTILRGEQ 91
Cdd:COG1958     9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEI----------------DDGEV------VRKLGTVVIRGDN 66

                  ...
gi 2078830397  92 ILS 94
Cdd:COG1958    67 VVF 69

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEervpktqldklrprkdskdgttLNIKVEKRVLGLTILRGEQ 91
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEE----------------------TIKDGEVRKLGLVLIRGNN 60

                  ...
gi 2078830397  92 ILS 94
Cdd:pfam01423  61 IVL 63

Like-Sm protein 8; 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 2078830397   9 SSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEervpktqldklrpRKDSKDGttlniKVEKRVLGLTILR 88
Cdd:cd01727     1 SSLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE-------------RVYSSDE-----GVEEVPLGLYLLR 62

                  ....
gi 2078830397  89 GEQI 92
Cdd:cd01727    63 GDNV 66

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        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERvpktqldklrprkdskdgttlnIKVEKRVLGLTILRGEQ 91
Cdd:cd00600     1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETG----------------------RDGKVRVLGLVLIRGSN 58

                  ...
gi 2078830397  92 ILS 94
Cdd:cd00600    59 IVS 61

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 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEErvpktqldkLRPRKDSkdgttLNIKVEKRVLGLTILRGEQ 91
Cdd:cd01729     7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEY---------LRDPEDP-----YKLTDETRSLGLVVCRGTS 72

                  ...
gi 2078830397  92 ILS 94
Cdd:cd01729    73 VVL 75

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
                  ....*....|....*....|....*....|....*....|....*....|..
gi 2078830397   8 HSSRLANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECIEERVPKTQLD 59
Cdd:cd01719     1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGEKTP 52

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 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFD-KHMNLVL 45
Cdd:cd11679     5 LNSLLDKEVIVTLSNGKTYTGQLVGFDpSSLNIVL 39

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 2078830397  23 LTQDGRVYI---------GQLMAFDKHMNLVLNEcIEERVpkTQLDklrprkdsKDGTTLN--IKVEKRVLGLTILRGEQ 91
Cdd:cd01730     8 LSLDERVYVklrgdrelrGRLHAYDQHLNMILGD-VEETI--TTVE--------IDEETYEeiYKTTKRNIPMLFVRGDG 76

                  .
gi 2078830397  92 I 92
Cdd:cd01730    77 V 77

Sm protein F; 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 F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.

                          10        20        30        40
                  ....*....|....*....|....*....|....*....|..
gi 2078830397  12 LANLIDYKLRVLTQDGRVYIGQLMAFDKHMNLVLNECiEERV 53
Cdd:cd01722     6 LNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANT-EEYI 46