Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEetvttvEIDEEtyeevykTAKRTIPMLFVRGDGVILVS 97
Cdd:COG1958    5 PLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAE------EIDDG-------EVVRKLGTVVIRGDNVVFIS 71

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362412    20 DLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIdeetyeevyktaKRTIPMLFVRGDGVILVSP 98
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK------------KRKLGLVFIRGNNIVYIIL 67

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEetvttvEIDEEtyeevykTAKRTIPMLFVRGDGVILVS 97
Cdd:cd01731    2 PLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAE------EIIEG-------ESVRKLGTVLVRGDNVVFIS 68

                 .
gi 281362412  98 P 98
Cdd:cd01731   69 P 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
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362412   20 DLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTtveideetyeevyKTAKRTIPMLFVRGDGVILVSP 98
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIK-------------DGEVRKLGLVLIRGNNIVLISP 66

Sm protein D2; 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 D2 heterodimerizes with subunit D1 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing D2, D3, E, F, and G subunits.

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEK--VYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYKTAKRTIPMLFVRGDGVIL 95
Cdd:cd01720    5 PLSLLTQSVKNNtqVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSKPVNKDRFISKMFLRGDSVIL 84

                 ....
gi 281362412  96 VSPP 99
Cdd:cd01720   85 VLRN 88

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 281362412  25 SLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEideetyeevyktaKRTIPMLFVRGDGVILVS 97
Cdd:cd00600    4 FIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGK-------------VRVLGLVLIRGSNIVSIR 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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281362412  32 VKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEvyKTAKRTIPMLFVRGDGVILVS 97
Cdd:cd01717   15 VTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEE--REEKRVLGLVLLRGENVVSMT 78

Like-Sm protein 5; 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
                 ....*....|....*....|....*....|....*....|....*....|....
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEET 71
Cdd:cd01732    4 PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKIT 57

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 281362412  26 LDEKVYVKMRNERELRGRLHAFDQHLNMVLgdaeetvttveidEETYEEVYKTAKRTIPMLFVRGDGVILV 96
Cdd:cd01719    9 MDKRLSLKLNGNRKVSGVLRGFDPFMNLVL-------------DDAVEEVGDGEKTPIGMVVIRGNSIIMI 66

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
                 ....*....|....*....|....*....|....*....|....*.
gi 281362412  26 LDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEET 71
Cdd:cd06168    8 LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEE 53

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        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEKVYVKMR-NERELRGRLHAFDQHLNMVLGDAEETVTTVEIdeetyeevyktakRTIPMLFVRGDGVILV 96
Cdd:cd11678    1 PNKKVKSLVGSRIRVEMKgDENQLQGRLVAVDDYMNLHLTDTMECVGEEKV-------------RSLGTVVLRGNNILLI 67

                 ..
gi 281362412  97 SP 98
Cdd:cd11678   68 QP 69