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Conserved domains on  [gi|15229773|ref|NP_187757|]
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Small nuclear ribonucleoprotein family protein [Arabidopsis thaliana]

Protein Classification

small nuclear ribonucleoprotein Sm G( domain architecture ID 10109553)

small nuclear ribonucleoprotein Sm G which plays a role in pre-mRNA splicing as a core component of the SMN-Sm complex that mediates spliceosomal snRNP assembly and as a component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs), the building blocks of the spliceosome

CATH:  2.30.30.100
Gene Ontology:  GO:0030532|GO:0008380|GO:0000398|GO:0003723|GO:0000387
PubMed:  18687770|7744013|11259661

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 6-74 2.78e-39

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.


:

Pssm-ID: 212466  Cd Length: 70  Bit Score: 124.17  E-value: 2.78e-39
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229773  6 QPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDD-KTDIGMVVIRGNSIVTVEALE 74
Cdd:cd01719  1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGeKTPIGMVVIRGNSIIMIEALD 70
 
Name Accession Description Interval E-value
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 6-74 2.78e-39

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.


Pssm-ID: 212466  Cd Length: 70  Bit Score: 124.17  E-value: 2.78e-39
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229773  6 QPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDD-KTDIGMVVIRGNSIVTVEALE 74
Cdd:cd01719  1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGeKTPIGMVVIRGNSIIMIEALD 70
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 8-71 6.96e-20

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.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 74.85  E-value: 6.96e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15229773    8 PDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDD-KTDIGMVVIRGNSIVTVE 71
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGeVRKLGLVLIRGNNIVLIS 65
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 8-72 5.00e-19

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 72.91  E-value: 5.00e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15229773     8 PDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEV--NGDDKTDIGMVVIRGNSIVTVEA 72
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETvkDGEKKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
10-70 4.11e-15

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 62.90  E-value: 4.11e-15
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDKTD-IGMVVIRGNSIVTV 70
Cdd:COG1958  9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRkLGTVVIRGDNVVFI 70
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 10-70 7.80e-09

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 47.30  E-value: 7.80e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229773  10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEV-NGDDKTDIGMVVIRGNSIVTV 70
Cdd:PRK00737  9 LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIqDGEVVRKLGKVVIRGDNVVYV 70
 
Name Accession Description Interval E-value
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 6-74 2.78e-39

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.


Pssm-ID: 212466  Cd Length: 70  Bit Score: 124.17  E-value: 2.78e-39
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229773  6 QPPDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDD-KTDIGMVVIRGNSIVTVEALE 74
Cdd:cd01719  1 HPPELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGDGeKTPIGMVVIRGNSIIMIEALD 70
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 8-71 6.96e-20

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.


Pssm-ID: 426258  Cd Length: 66  Bit Score: 74.85  E-value: 6.96e-20
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 15229773    8 PDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDD-KTDIGMVVIRGNSIVTVE 71
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGeVRKLGLVLIRGNNIVLIS 65
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 8-72 5.00e-19

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 72.91  E-value: 5.00e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 15229773     8 PDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEV--NGDDKTDIGMVVIRGNSIVTVEA 72
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETvkDGEKKRKLGLVFIRGNNIVYIIL 67
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 9-70 1.23e-18

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.


Pssm-ID: 212476  Cd Length: 89  Bit Score: 72.62  E-value: 1.23e-18
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 15229773  9 DLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVE---------VNGDDKTDIGMVVIRGNSIVTV 70
Cdd:cd01729  6 DLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEylrdpedpyKLTDETRSLGLVVCRGTSVVLI 76
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
10-70 4.11e-15

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 62.90  E-value: 4.11e-15
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDKTD-IGMVVIRGNSIVTV 70
Cdd:COG1958  9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRkLGTVVIRGDNVVFI 70
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 10-71 1.14e-13

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.


Pssm-ID: 212462 [Multi-domain]  Cd Length: 63  Bit Score: 59.18  E-value: 1.14e-13
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDKT-DIGMVVIRGNSIVTVE 71
Cdd:cd00600  1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVrVLGLVLIRGSNIVSIR 63
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 10-70 3.09e-12

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.


Pssm-ID: 212474  Cd Length: 91  Bit Score: 56.38  E-value: 3.09e-12
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVE-----VNGDDKTDIGMVVIRGNSIVTV 70
Cdd:cd01727  4 LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHErvyssDEGVEEVPLGLYLLRGDNVAVI 69
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 10-70 3.99e-12

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.


Pssm-ID: 212478  Cd Length: 69  Bit Score: 55.27  E-value: 3.99e-12
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEV-NGDDKTDIGMVVIRGNSIVTV 70
Cdd:cd01731  6 LNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIiEGESVRKLGTVLVRGDNVVFI 67
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
 9-68 1.77e-11

Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring around the 3'-terminus of the gamma-methyl triphosphate (gamma-m-P3) capped U6 snRNA. Accumulation of uridylated RNAs in an lsm1 mutant suggests an involvement of the LSm1-7 complex in recognition of the 3' uridylation tag and recruitment of the decapping machinery. LSm1-7, together with Pat1, are also called the decapping activator. 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.


Pssm-ID: 212475  Cd Length: 74  Bit Score: 54.06  E-value: 1.77e-11
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15229773  9 DLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVE--VNGDDKTDI--GMVVIRGNSIV 68
Cdd:cd01728  6 SLEEELDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVEriIVGNQYGDIprGLFIIRGENVV 69
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 10-67 1.97e-09

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.


Pssm-ID: 212473  Cd Length: 68  Bit Score: 48.67  E-value: 1.97e-09
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*....
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVE-VNGDDKTDIGMVVIRGNSI 67
Cdd:cd01726  6 LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEyVDGQLVAKYGDAFIRGNNV 64
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 10-71 2.27e-09

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.


Pssm-ID: 212486  Cd Length: 73  Bit Score: 48.32  E-value: 2.27e-09
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDKTD------IGMVVIRGNSIVTVE 71
Cdd:cd06168  4 LRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGaeeprsLGLVMVPGKHIVSIE 71
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 10-70 7.80e-09

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 47.30  E-value: 7.80e-09
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229773  10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEV-NGDDKTDIGMVVIRGNSIVTV 70
Cdd:PRK00737  9 LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIqDGEVVRKLGKVVIRGDNVVYV 70
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 6-70 4.33e-08

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.


Pssm-ID: 212477  Cd Length: 82  Bit Score: 45.29  E-value: 4.33e-08
                       10        20        30        40        50        60        70        80
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 15229773  6 QPPDLKKY-MDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVE----VNGDDKT----------DIGMVVIRGNSIVTV 70
Cdd:cd01730  1 EPLDLIRLsLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEEtittVEIDEETyeeiykttkrNIPMLFVRGDGVILV 80
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 17-74 1.74e-07

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 43.95  E-value: 1.74e-07
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 15229773  17 KLQIKL--NANRMVVGTLRGFDQFMNLVVDNTVEVN--GDDKTDIGMVVIRGNSIVTVEALE 74
Cdd:PTZ00138 28 RVQIWLydHPNLRIEGKILGFDEYMNMVLDDAEEVYtkKNTRKDLGRILLKGDNITLIMAAK 89
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 10-73 4.74e-07

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.


Pssm-ID: 212464  Cd Length: 80  Bit Score: 42.92  E-value: 4.74e-07
                       10        20        30        40        50        60        70
               ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 15229773 10 LKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEV------------NGDDKTDIGMVVIRGNSIVTVEAL 73
Cdd:cd01717  5 MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFrkikpkkkkkgeEREEKRVLGLVLLRGENVVSMTVE 80
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 8-70 1.52e-06

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.


Pssm-ID: 212469  Cd Length: 69  Bit Score: 41.04  E-value: 1.52e-06
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15229773  8 PDLKKYMDKKLQIKLNANRMVVGTLRGFDQFMNLVVDNTVE-VNGDDKTDIGMVVIRGNSIVTV 70
Cdd:cd01722  4 PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEyIDGKFTGNLGEVLIRCNNVLYI 67
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 30-67 6.56e-06

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.


Pssm-ID: 212465  Cd Length: 79  Bit Score: 39.84  E-value: 6.56e-06
                       10        20        30        40
               ....*....|....*....|....*....|....*....|
gi 15229773 30 GTLRGFDQFMNLVVDNTVEVNGDDKT--DIGMVVIRGNSI 67
Cdd:cd01718 35 GKIIGFDEYMNLVLDDAEEVHLKTNTrkPLGRILLKGDNI 74
archaeal_LSm cd11678
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ...
 10-71 7.81e-06

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.


Pssm-ID: 212489  Cd Length: 69  Bit Score: 39.41  E-value: 7.81e-06
                       10        20        30        40        50        60
               ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 15229773 10 LKKYMDKKLQIKLNAN-RMVVGTLRGFDQFMNLVVDNTVEVNGDDKT-DIGMVVIRGNSIVTVE 71
Cdd:cd11678  5 VKSLVGSRIRVEMKGDeNQLQGRLVAVDDYMNLHLTDTMECVGEEKVrSLGTVVLRGNNILLIQ 68
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 17-67 1.34e-04

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.


Pssm-ID: 212479 [Multi-domain]  Cd Length: 76  Bit Score: 36.45  E-value: 1.34e-04
                       10        20        30        40        50
               ....*....|....*....|....*....|....*....|....*....|....*
gi 15229773 17 KLQIKLNANRMVVGTLRGFDQFMNLVVDNTVEVNGDDK----TDIGMVVIRGNSI 67
Cdd:cd01732 15 KIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEgrkiTKLDQILLNGNNI 69
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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