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 17543872  16 EPLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREVDEDTFEEIYKQTKRVVPMLFVRGDSVILV 95
Cdd:cd01730   1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILV 80

                ..
gi 17543872  96 SP 97
Cdd:cd01730  81 SP 82

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 17543872  16 EPLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREVDEDTFEEIYKQTKRVVPMLFVRGDSVILV 95
Cdd:cd01730   1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILV 80

                ..
gi 17543872  96 SP 97
Cdd:cd01730  81 SP 82

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17543872  14 VEEPLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITtrevdedtfeeiyKQTKRVVPMLFVRGDSVI 93
Cdd:COG1958   2 SERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDD-------------GEVVRKLGTVVIRGDNVV 68

                ...
gi 17543872  94 LVS 96
Cdd:COG1958  69 FIS 71

small nuclear ribonucleoprotein; Provisional

                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17543872   14 VEEPLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITtrevdedtfeeiyKQTKRVVPMLFVRGDSVI 93
Cdd:PRK00737   2 AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQD-------------GEVVRKLGKVVIRGDNVV 68

                 ....
gi 17543872   94 LVSP 97
Cdd:PRK00737  69 YVSP 72

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 17543872  16 EPLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREVDEDTFEEIYKQTKRVVPMLFVRGDSVILV 95
Cdd:cd01730   1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILV 80

                ..
gi 17543872  96 SP 97
Cdd:cd01730  81 SP 82

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 17543872    19 DLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREvdedtfeeiykqtKRVVPMLFVRGDSVILVSP 97
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGE-------------VRKLGLVLIRGNNIVLISP 66

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

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 17543872     19 DLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREVdedtfeeiykqtKRVVPMLFVRGDSVILVSP 97
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK------------KRKLGLVFIRGNNIVYIIL 67

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 17543872  17 PLDLLRLSL--DERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTREVDEDTFEEIYKQTKRVVPMLFVRGDSVIL 94
Cdd:cd01720   5 PLSLLTQSVknNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMWTEVPKTGKGKKSKPVNKDRFISKMFLRGDSVIL 84

                ....
gi 17543872  95 VSPP 98
Cdd:cd01720  85 VLRN 88

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 17543872  18 LDLLRLsLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITtrevDEDTFEEIYKQTkRVVPMLFVRGDSVILVSP 97
Cdd:cd01729   5 LDLSKY-VDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLR----DPEDPYKLTDET-RSLGLVVCRGTSVVLISP 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
                ....*....|....*....|....*....|....*....|....*....
gi 17543872  17 PLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITTRE 65
Cdd:cd01732   4 PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPE 52

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        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17543872  17 PLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLseveetittrevdEDTFEEIYKQTKRVVPMLFVRGDSVILVS 96
Cdd:cd01726   2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVL-------------EDTEEYVDGQLVAKYGDAFIRGNNVLYIS 68

Like-Sm protein 11, middle domain; 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. LSm11 is an SmD2-like subunit which binds U7 snRNA along with LSm10 and five other Sm subunits to form a 7-membered ring structure. LSm11 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.

                        10        20        30        40
                ....*....|....*....|....*....|....*....|.
gi 17543872  28 RVYVKMRNDRELRGR----LRAFDQHLNMVLSEVEETITTR 64
Cdd:cd01739  10 RVKVYIRKAKGIRGScegyLVAFDKHWNLALVDVDETWTRR 50

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        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 17543872  17 PLDLLRLSLDERVYVKMRNDRELRGRLRAFDQHLNMVLSEVEETITtrevDEDTFEEIykqtkrvvPMLFVRGDSVILVS 96
Cdd:cd01723   2 PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICTSK----DGDRFWKM--------PECYIRGNTIKYLR 69

                ..
gi 17543872  97 PP 98
Cdd:cd01723  70 LP 71

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 17543872  25 LDERVYVKMRND-RELRGRLRAFDQHLNMVLseveetittrevdEDTFEEIYKQTKRVVPMLFVRGDSVILVSP 97
Cdd:cd11678   9 VGSRIRVEMKGDeNQLQGRLVAVDDYMNLHL-------------TDTMECVGEEKVRSLGTVVLRGNNILLIQP 69