Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490133836  5 NVQRPLDALGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYIS 75
Cdd:COG1958   1 MSERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNVVFIS 71

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
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 490133836  13 LGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYISP 76
Cdd:pfam01423  3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];

                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490133836  5 NVQRPLDALGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYIS 75
Cdd:COG1958   1 MSERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNVVFIS 71

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490133836  8 RPLDALGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYIS 75
Cdd:cd01726   1 TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGNNVLYIS 68

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

                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 490133836   13 LGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEE-LQDGEVTRRLGVVLIRGDNIVYISP 76
Cdd:smart00651  3 LKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEEtVKDGEKKRKLGLVFIRGNNIVYIIL 67

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        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490133836 13 LGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYI 74
Cdd:cd01722   6 LNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNNVLYI 67

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 490133836 13 LGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEE-LQD-------GEVTRRLGVVLIRGDNIVYISP 76
Cdd:cd01729   7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEyLRDpedpyklTDETRSLGLVVCRGTSVVLISP 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        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490133836  9 PLDALGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRR---LGVVLIRGDNIVYISP 76
Cdd:cd01732   4 PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKitkLDQILLNGNNIAMLVP 74

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 490133836  9 PLDALGKSVNSPVLIKLKGD-REFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYISP 76
Cdd:cd11678   1 PNKKVKSLVGSRIRVEMKGDeNQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLIQP 69

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        60
                ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 490133836 19 SPVLIKLKGDREFR--GILKSFDLHMNLVLNDAEELQDGEVTRR-LGVVLIRGDNIVYISP 76
Cdd:cd01718  19 SRVQIWLYEQTDMRieGKIIGFDEYMNLVLDDAEEVHLKTNTRKpLGRILLKGDNITLIQN 79

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 490133836  9 PLDALGKSVNSPVLIKLKGDREFRGILKSFDLHMNLVLNDA-EELQDGEVTRRLGVVLIRGDNIVYIS 75
Cdd:cd01723   2 PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNViCTSKDGDRFWKMPECYIRGNTIKYLR 69

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
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 490133836 13 LGKSVNSPVLIkLKGD-REFRGILKSFDLHMNLVLNDAEE----LQDGEVTRRLGVVLIRGDNIVYI 74
Cdd:cd01727   4 LEDYLNKRVVV-ITTDgRVIVGTLKGFDQTTNLILSNCHErvysSDEGVEEVPLGLYLLRGDNVAVI 69

Like-Sm protein 10; 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. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 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        50
                ....*....|....*....|....*....|....*....|....*....|....*...
gi 490133836 17 VNSPVLIKLKGDREFRGILKSFDLHMNLVLNDAEELQDGEVTRRLGVVLIRGDNIVYI 74
Cdd:cd01733  18 QGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFTDRRGKQHHFDEFFVQGRNIRYV 75