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Conserved domains on  [gi|281362412|ref|NP_001163707|]
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uncharacterized protein Dmel_CG31184 [Drosophila melanogaster]

Protein Classification

U6 snRNA-associated Sm-like protein LSm3( domain architecture ID 10109609)

U6 snRNA-associated Sm-like protein LSm3 plays a role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP complex that is involved in spliceosome assembly, and as a component of the precatalytic spliceosome (spliceosome B complex)

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
17-98 7.50e-54

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: 162.39  E-value: 7.50e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  17 EPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYKTAKRTIPMLFVRGDGVILV 96
Cdd:cd01730    1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILV 80

                 ..
gi 281362412  97 SP 98
Cdd:cd01730   81 SP 82
 
Name Accession Description Interval E-value
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
17-98 7.50e-54

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: 162.39  E-value: 7.50e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  17 EPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYKTAKRTIPMLFVRGDGVILV 96
Cdd:cd01730    1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILV 80

                 ..
gi 281362412  97 SP 98
Cdd:cd01730   81 SP 82
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
18-97 4.74e-18

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 71.37  E-value: 4.74e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEetvttvEIDEEtyeevykTAKRTIPMLFVRGDGVILVS 97
Cdd:COG1958    5 PLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAE------EIDDG-------EVVRKLGTVVIRGDNVVFIS 71
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
20-98 1.06e-17

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: 70.23  E-value: 1.06e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362412   20 DLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTtveideetyeevyKTAKRTIPMLFVRGDGVILVSP 98
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIK-------------DGEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
20-98 2.30e-16

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 67.13  E-value: 2.30e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362412    20 DLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIdeetyeevyktaKRTIPMLFVRGDGVILVSP 98
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK------------KRKLGLVFIRGNNIVYIIL 67
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
15-98 1.42e-13

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 60.01  E-value: 1.42e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  15 VKEPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETvttveIDEETyeevyktaKRTIPMLFVRGDGVI 94
Cdd:PRK00737   2 AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGEV--------VRKLGKVVIRGDNVV 68

                 ....
gi 281362412  95 LVSP 98
Cdd:PRK00737  69 YVSP 72
 
Name Accession Description Interval E-value
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
17-98 7.50e-54

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: 162.39  E-value: 7.50e-54
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  17 EPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYKTAKRTIPMLFVRGDGVILV 96
Cdd:cd01730    1 EPLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETITTVEIDEETYEEIYKTTKRNIPMLFVRGDGVILV 80

                 ..
gi 281362412  97 SP 98
Cdd:cd01730   81 SP 82
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
18-98 3.45e-20

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: 76.84  E-value: 3.45e-20
                         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
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
18-97 4.74e-18

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 71.37  E-value: 4.74e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEetvttvEIDEEtyeevykTAKRTIPMLFVRGDGVILVS 97
Cdd:COG1958    5 PLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAE------EIDDG-------EVVRKLGTVVIRGDNVVFIS 71
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
20-98 1.06e-17

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: 70.23  E-value: 1.06e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362412   20 DLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTtveideetyeevyKTAKRTIPMLFVRGDGVILVSP 98
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIK-------------DGEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
20-98 2.30e-16

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 67.13  E-value: 2.30e-16
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281362412    20 DLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIdeetyeevyktaKRTIPMLFVRGDGVILVSP 98
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEK------------KRKLGLVFIRGNNIVYIIL 67
Sm_D2 cd01720
Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
18-99 3.74e-14

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.


Pssm-ID: 212467  Cd Length: 89  Bit Score: 61.96  E-value: 3.74e-14
                         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
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
15-98 1.42e-13

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 60.01  E-value: 1.42e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  15 VKEPLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETvttveIDEETyeevyktaKRTIPMLFVRGDGVI 94
Cdd:PRK00737   2 AQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEI-----QDGEV--------VRKLGKVVIRGDNVV 68

                 ....
gi 281362412  95 LVSP 98
Cdd:PRK00737  69 YVSP 72
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
25-97 1.06e-11

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: 54.95  E-value: 1.06e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 281362412  25 SLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEideetyeevyktaKRTIPMLFVRGDGVILVS 97
Cdd:cd00600    4 FIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGK-------------VRVLGLVLIRGSNIVSIR 63
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
19-98 4.02e-08

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: 46.42  E-value: 4.02e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  19 LDLIRLsLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEvyktaKRTIPMLFVRGDGVILVSP 98
Cdd:cd01729    5 LDLSKY-VDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDE-----TRSLGLVVCRGTSVVLISP 78
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
32-97 2.15e-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: 44.46  E-value: 2.15e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281362412  32 VKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEvyKTAKRTIPMLFVRGDGVILVS 97
Cdd:cd01717   15 VTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKGEE--REEKRVLGLVLLRGENVVSMT 78
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
18-97 1.57e-06

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: 42.12  E-value: 1.57e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIdeETYEEVyktakrtipmlFVRGDGVILVS 97
Cdd:cd01726    2 PSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLV--AKYGDA-----------FIRGNNVLYIS 68
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
18-71 7.59e-06

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: 40.31  E-value: 7.59e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 281362412  18 PLDLIRLSLDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEET 71
Cdd:cd01732    4 PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKIT 57
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
26-96 9.25e-06

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: 40.19  E-value: 9.25e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362412  26 LDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEETYEEVYktakrtipmlFVRGDGVILV 96
Cdd:cd01728   11 LDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERIIVGNQYGDIPRGLF----------IIRGENVVLL 71
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
26-96 4.97e-05

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: 38.27  E-value: 4.97e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281362412  26 LDEKVYVKMRNERELRGRLHAFDQHLNMVLgdaeetvttveidEETYEEVYKTAKRTIPMLFVRGDGVILV 96
Cdd:cd01719    9 MDKRLSLKLNGNRKVSGVLRGFDPFMNLVL-------------DDAVEEVGDGEKTPIGMVVIRGNSIIMI 66
LSm11_M cd01739
Like-Sm protein 11, middle domain; The eukaryotic Sm and Sm-like (LSm) proteins associate with ...
29-63 5.53e-05

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.


Pssm-ID: 212485  Cd Length: 63  Bit Score: 38.01  E-value: 5.53e-05
                         10        20        30
                 ....*....|....*....|....*....|....*....
gi 281362412  29 KVYVkmRNERELRGR----LHAFDQHLNMVLGDAEETVT 63
Cdd:cd01739   12 KVYI--RKAKGIRGScegyLVAFDKHWNLALVDVDETWT 48
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
26-71 1.23e-04

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: 37.15  E-value: 1.23e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 281362412  26 LDEKVYVKMRNERELRGRLHAFDQHLNMVLGDAEETVTTVEIDEET 71
Cdd:cd06168    8 LGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSDLGAEE 53
archaeal_Sm_like cd11679
archaeal Sm-related protein; Archaeal Sm-related proteins: The Sm proteins are conserved in ...
26-59 4.52e-03

archaeal Sm-related protein; Archaeal Sm-related 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: 212490  Cd Length: 65  Bit Score: 33.01  E-value: 4.52e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 281362412  26 LDEKVYVKMRNERELRGRLHAFDQH-LNMVLGDAE 59
Cdd:cd11679    9 LDKEVIVTLSNGKTYTGQLVGFDPSsLNIVLTNAK 43
archaeal_LSm cd11678
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ...
18-98 5.01e-03

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: 32.86  E-value: 5.01e-03
                         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
 
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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