Conserved Protein Domain Family
LSM

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pfam01423: LSM 
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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.
Statistics
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PSSM-Id: 307537
View PSSM: pfam01423
Aligned: 114 rows
Threshold Bit Score: 40.1835
Threshold Setting Gi: 75270410
Created: 13-Jul-2016
Updated: 4-Aug-2016
Structure
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Program:
Drawing:
Aligned Rows:
PubMed ReferencesClick to see Conserved Features Help

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
3JB9_D         6 KLLHETQGHIVTMELENGS-TYRGKLIEAEDNMNCQMRDISvtardg----rvshlDQVYIRGSHIRFLIV 71
gi 123791637  19 ILLQGLQGQITTVDLRDES-VARGRIDNVDAFMNIRLANVTytdrwg----hqvelDDLFVTGRNVRYVHI 84
gi 74644154   16 QFLQRMKNRSVRVALKWGQ-VYEGTLVASDNYFNILLDECTerege-----asvkiGEVSIRCNNIKRICE 80
gi 75270411    5 NILNNNYNKNVFVKLKWGS-SYTGIFIGSDNYMNIILDSCSeviteq----nlgflGLVLIRCNNILFISF 70
4M75_D        14 EFLSDIIGKTVNVKLASGL-LYSGRLESIDGFXNVALSSATehyesnnnkllnkfnSDVFLRGTQVXYISE 83
gi 74823936   11 DFLKLIIGRPVVVKLNSGA-DYRGVLISLDGYMNVVLEQTEeyvegq----lknkyGDTFIRGNNVFYIST 76
4EMK_B         7 EFLNKVIGKKVLIRLSSGV-DYKGILSCLDGYXNLALERTEeyvngk----ktnvyGDAFIRGNNVLYVSA 72
gi 75020103    9 EFLKKVIGKPVVVKLNSGV-DYRGILACLDGYMNIALEQTEeysngq----lqnkyGDAFIRGNNVLYIST 74
gi 594053720  86 PFLNGLTGKPVMVKLKWGM-EYKGYLVSVDGYMNMQLANTEeyidga----lsghlGEVLIRCNNVLYIrg 151
gi 85080344   10 PFLQDLVNSFVTIRLKWGEtEYVGRLVSIDSYMNIQLSDTKeyinrk----ftgalGQVLIRCNNVLYIkk 76
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