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Conserved domains on  [gi|499332638|ref|WP_011023130|]
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MULTISPECIES: LSm family protein [Methanosarcina]

Protein Classification

LSm family protein( domain architecture ID 10792055)

LSm family protein such as LSm archaeal proteins (also known as SmAPs) that interact with polynucleotide phosphorylase P and uridine-rich RNA sequences, and, may be involved in the processing of tRNAs; contains an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus

Gene Ontology:  GO:0006396
PubMed:  33827399

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 1-72 1.39e-41

small nuclear ribonucleoprotein; Provisional


:

Pssm-ID: 179104  Cd Length: 72  Bit Score: 129.73  E-value: 1.39e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499332638  1 MANRPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:PRK00737  1 MAQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP 72
 
Name Accession Description Interval E-value
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 1-72 1.39e-41

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 129.73  E-value: 1.39e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499332638  1 MANRPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:PRK00737  1 MAQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP 72
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
1-71 3.62e-34

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 111.05  E-value: 3.62e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499332638  1 MANRPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVS 71
Cdd:COG1958   1 MSERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNVVFIS 71
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 4-72 6.37e-32

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: 105.35  E-value: 6.37e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499332638  4 RPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:cd01731   1 RPLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFISP 69
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 7-72 6.03e-21

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: 77.16  E-value: 6.03e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499332638   7 DILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 7-72 1.11e-19

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 74.07  E-value: 1.11e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499332638    7 DILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEE-LRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEEtVKDGEKKRKLGLVFIRGNNIVYIIL 67
 
Name Accession Description Interval E-value
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 1-72 1.39e-41

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 129.73  E-value: 1.39e-41
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499332638  1 MANRPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:PRK00737  1 MAQRPLDVLNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEVVRKLGKVVIRGDNVVYVSP 72
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
1-71 3.62e-34

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 111.05  E-value: 3.62e-34
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499332638  1 MANRPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVS 71
Cdd:COG1958   1 MSERPLKVLEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDGEVVRKLGTVVIRGDNVVFIS 71
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 4-72 6.37e-32

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: 105.35  E-value: 6.37e-32
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499332638  4 RPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:cd01731   1 RPLDVLNESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEGESVRKLGTVLVRGDNVVFISP 69
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 4-71 2.95e-21

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: 78.33  E-value: 2.95e-21
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499332638  4 RPLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVS 71
Cdd:cd01726   1 TPSKFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVDGQLVAKYGDAFIRGNNVLYIS 68
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 7-72 6.03e-21

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: 77.16  E-value: 6.03e-21
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499332638   7 DILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 7-72 1.11e-19

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 74.07  E-value: 1.11e-19
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499332638    7 DILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEE-LRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEEtVKDGEKKRKLGLVFIRGNNIVYIIL 67
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 9-71 6.26e-14

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: 59.57  E-value: 6.26e-14
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499332638  9 LNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVS 71
Cdd:cd00600   1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVLGLVLIRGSNIVSIR 63
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 5-70 1.07e-13

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: 59.15  E-value: 1.07e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 499332638  5 PLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYV 70
Cdd:cd01722   2 PKPFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYIDGKFTGNLGEVLIRCNNVLYI 67
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 9-72 5.69e-13

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: 57.98  E-value: 5.69e-13
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 499332638  9 LNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEE-LRDGEVVSKFS-------SVVIRGDNVVYVSP 72
Cdd:cd01729   7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEyLRDPEDPYKLTdetrslgLVVCRGTSVVLISP 78
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 5-72 1.55e-12

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: 56.47  E-value: 1.55e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499332638  5 PLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEEL-----RDGEVVSKFSSVV--------IRGDNVVYVS 71
Cdd:cd01730   2 PLDLIRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETittveIDEETYEEIYKTTkrnipmlfVRGDGVILVS 81


                .
gi 499332638 72 P 72
Cdd:cd01730  82 P 82
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 9-70 1.08e-10

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: 51.36  E-value: 1.08e-10
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499332638  9 LNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNA-EELRDGEVVsKFSSVVIRGDNVVYV 70
Cdd:cd01719   5 LKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAvEEVGDGEKT-PIGMVVIRGNSIIMI 66
archaeal_LSm cd11678
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ...
 5-72 1.39e-08

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: 46.35  E-value: 1.39e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 499332638  5 PLDILNNALDTPVIVRLKG-AREFRGELKGYDIHMNLVLDNAEELRDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:cd11678   1 PNKKVKSLVGSRIRVEMKGdENQLQGRLVAVDDYMNLHLTDTMECVGEEKVRSLGTVVLRGNNILLIQP 69
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 5-71 2.44e-08

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.


Pssm-ID: 212470 [Multi-domain]  Cd Length: 76  Bit Score: 45.64  E-value: 2.44e-08
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 499332638  5 PLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNA-EELRDGEVVSKFSSVVIRGDNVVYVS 71
Cdd:cd01723   2 PLSLLRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNViCTSKDGDRFWKMPECYIRGNTIKYLR 69
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 19-71 3.58e-06

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: 40.23  E-value: 3.58e-06
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 499332638 19 VRLKGAREFRGELKGYDIHMNLVLDNAEELR-----------DGEVVSKFSSVVIRGDNVVYVS 71
Cdd:cd01717  15 VTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRkikpkkkkkgeEREEKRVLGLVLLRGENVVSMT 78
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 5-72 4.19e-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: 39.92  E-value: 4.19e-06
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 499332638  5 PLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEEL---RDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:cd01732   4 PLELIDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYeitPEGRKITKLDQILLNGNNIAMLVP 74
LSm1 cd01728
Like-Sm protein 1; The eukaryotic LSm proteins (LSm1-7) assemble into a hetero-heptameric ring ...
 13-70 1.15e-05

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: 38.65  E-value: 1.15e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499332638 13 LDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEELRDgeVVSKFSSV-----VIRGDNVVYV 70
Cdd:cd01728  11 LDKKILVVLRDGRKLIGILRSFDQFANLVLEDTVERII--VGNQYGDIprglfIIRGENVVLL 71
archaeal_Sm_like cd11679
archaeal Sm-related protein; Archaeal Sm-related proteins: The Sm proteins are conserved in ...
 9-70 3.98e-05

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: 37.25  E-value: 3.98e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 499332638  9 LNNALDTPVIVRLKGAREFRGELKGYDIH-MNLVLDNAEElRDGEvvsKFSSVVIRGDNVVYV 70
Cdd:cd11679   5 LNSLLDKEVIVTLSNGKTYTGQLVGFDPSsLNIVLTNAKD-SSGN---KFPKVIINGNRISEI 63
Sm_D3 cd01721
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 5-70 4.24e-05

Sm protein D3; 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 D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits.


Pssm-ID: 212468  Cd Length: 70  Bit Score: 37.12  E-value: 4.24e-05
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 499332638  5 PLDILNNALDTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEEL-RDGEvVSKFSSVVIRGDNVVYV 70
Cdd:cd01721   1 PIKLLHEAEGHIVTVELKTGEVYRGKLIEAEDNMNCQLKDVTVTaRDGK-VSKLEQVYIRGSQIRFI 66
Sm_D2 cd01720
Sm protein D2; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 5-72 1.42e-04

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: 36.54  E-value: 1.42e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 499332638  5 PLDILNNAL--DTPVIVRLKGAREFRGELKGYDIHMNLVLDNAEEL-----RDGE-----VVSK---FSSVVIRGDNVVY 69
Cdd:cd01720   5 PLSLLTQSVknNTQVLINCRNNKKLLARVKAFDRHCNMVLENVKEMwtevpKTGKgkkskPVNKdrfISKMFLRGDSVIL 84


                ...
gi 499332638 70 VSP 72
Cdd:cd01720  85 VLR 87
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 29-71 1.61e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 36.24  E-value: 1.61e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....
gi 499332638 29 GELKGYDIHMNLVLDNAEEL-RDGEVVSKFSSVVIRGDNVVYVS 71
Cdd:PTZ00138 43 GKILGFDEYMNMVLDDAEEVyTKKNTRKDLGRILLKGDNITLIM 86
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 29-72 2.70e-04

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: 35.22  E-value: 2.70e-04
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 499332638 29 GELKGYDIHMNLVLDNAEEL-RDGEVVSKFSSVVIRGDNVVYVSP 72
Cdd:cd01718  35 GKIIGFDEYMNLVLDDAEEVhLKTNTRKPLGRILLKGDNITLIQN 79
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 24-68 1.30e-03

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: 34.04  E-value: 1.30e-03
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*....
gi 499332638 24 AREFRGELKGYDIHMNLVLDNAEE--LRDGEVVSKFSS--VVIRGDNVV 68
Cdd:cd01727  19 GRVIVGTLKGFDQTTNLILSNCHErvYSSDEGVEEVPLglYLLRGDNVA 67
 
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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