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Conserved domains on  [gi|1938929012]
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Chain h, Small nuclear ribonucleoprotein Sm D1

Protein Classification

LSm family protein( domain architecture ID 249)

LSm family protein such as eukaryotic LSm (Sm-like proteins) and bacterial LSm-related Hfq proteins, that have an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and are involved in processes associated with RNA processing and gene expression regulation

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_like super family cl00259
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 2-111 2.87e-37

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.


The actual alignment was detected with superfamily member cd01724:

Pssm-ID: 469694  Cd Length: 92  Bit Score: 122.72  E-value: 2.87e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   2 KLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPqprlnklnsngiamaslyltgGQQPTasdniaS 81
Cdd:cd01724     1 KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLK---------------------GKNPV------S 53

                          90       100       110
                  ....*....|....*....|....*....|
gi 1938929012  82 LQYINIRGNTIRQIILPDSLNLDSLLVDQK 111
Cdd:cd01724    54 LDTLSIRGNNIRYIILPDSLNLDTLLVDDT 83
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-111 2.87e-37

Sm protein D1; 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 D1 heterodimerizes with subunit D2 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 DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 122.72  E-value: 2.87e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   2 KLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPqprlnklnsngiamaslyltgGQQPTasdniaS 81
Cdd:cd01724     1 KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLK---------------------GKNPV------S 53

                          90       100       110
                  ....*....|....*....|....*....|
gi 1938929012  82 LQYINIRGNTIRQIILPDSLNLDSLLVDQK 111
Cdd:cd01724    54 LDTLSIRGNNIRYIILPDSLNLDTLLVDDT 83
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-97 7.51e-14

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 62.13  E-value: 7.51e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012    5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPrlnklnsngiamaslyltggqqptasDNIASLQY 84
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG--------------------------EKKRKLGL 54

                           90
                   ....*....|...
gi 1938929012   85 INIRGNTIRQIIL 97
Cdd:smart00651  55 VFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 5-97 2.70e-12

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: 57.90  E-value: 2.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNsngiamaslyltggqqptasdniaslqY 84
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLG---------------------------L 53

                          90
                  ....*....|...
gi 1938929012  85 INIRGNTIRQIIL 97
Cdd:pfam01423  54 VLIRGNNIVLISP 66
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
7-43 1.03e-06

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 43.64  E-value: 1.03e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1938929012   7 LKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDV 43
Cdd:COG1958     9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDA 45
 
Name Accession Description Interval E-value
Sm_D1 cd01724
Sm protein D1; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 2-111 2.87e-37

Sm protein D1; 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 D1 heterodimerizes with subunit D2 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 DB, D3, E, F, and G subunits.


Pssm-ID: 212471  Cd Length: 92  Bit Score: 122.72  E-value: 2.87e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   2 KLVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPqprlnklnsngiamaslyltgGQQPTasdniaS 81
Cdd:cd01724     1 KLVRFLMKLSNETVTIELKNGTVVHGTITGVDVSMNTHLKNVKLTLK---------------------GKNPV------S 53

                          90       100       110
                  ....*....|....*....|....*....|
gi 1938929012  82 LQYINIRGNTIRQIILPDSLNLDSLLVDQK 111
Cdd:cd01724    54 LDTLSIRGNNIRYIILPDSLNLDTLLVDDT 83
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 5-97 7.51e-14

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 62.13  E-value: 7.51e-14
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012    5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPrlnklnsngiamaslyltggqqptasDNIASLQY 84
Cdd:smart00651   1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDG--------------------------EKKRKLGL 54

                           90
                   ....*....|...
gi 1938929012   85 INIRGNTIRQIIL 97
Cdd:smart00651  55 VFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 5-97 2.70e-12

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: 57.90  E-value: 2.70e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKLNsngiamaslyltggqqptasdniaslqY 84
Cdd:pfam01423   1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRKLG---------------------------L 53

                          90
                  ....*....|...
gi 1938929012  85 INIRGNTIRQIIL 97
Cdd:pfam01423  54 VLIRGNNIVLISP 66
Sm_D3 cd01721
Sm protein D3; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 15-99 5.38e-07

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: 44.43  E-value: 5.38e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012  15 VTIELKNGTTVWGTLQSVSPQMNAILTDVKLTlpqprlnklNSNGiamaslyltggqqptasdNIASLQYINIRGNTIRQ 94
Cdd:cd01721    13 VTVELKTGEVYRGKLIEAEDNMNCQLKDVTVT---------ARDG------------------KVSKLEQVYIRGSQIRF 65


                  ....*
gi 1938929012  95 IILPD 99
Cdd:cd01721    66 IILPD 70
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
7-43 1.03e-06

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 43.64  E-value: 1.03e-06
                          10        20        30
                  ....*....|....*....|....*....|....*..
gi 1938929012   7 LKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDV 43
Cdd:COG1958     9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDA 45
LSm2 cd01725
Like-Sm protein 2; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 5-100 1.29e-06

Like-Sm protein 2; 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: 212472  Cd Length: 89  Bit Score: 43.73  E-value: 1.29e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQpRLNKLNSngiamaslyltggqqptasdniasLQY 84
Cdd:cd01725     4 SFFKTLVGKEVTVELKNDLSITGTLHSVDQYLNIKLTNISVNDPE-KYPHLLS------------------------VKN 58

                          90
                  ....*....|....*.
gi 1938929012  85 INIRGNTIRQIILPDS 100
Cdd:cd01725    59 CFIRGSVVRYVQLPAD 74
LSm10 cd01733
Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form ...
 3-46 3.10e-06

Like-Sm protein 10; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-membered ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.


Pssm-ID: 212480  Cd Length: 78  Bit Score: 42.53  E-value: 3.10e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1938929012   3 LVNFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLT 46
Cdd:cd01733    10 LVCLLQALQGRVTTVELRNETSVRGIIDNVDGFMNITLSDATFT 53
LSm4 cd01723
Like-Sm protein 4; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 7-101 9.65e-06

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: 41.41  E-value: 9.65e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1938929012   7 LKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTlpqprlNKLNSNGIAMASLYltggqqptasdniaslqyin 86
Cdd:cd01723     6 LRTAQGHPVLVELKNGETYNGHLVNCDNWMNIHLKNVICT------SKDGDRFWKMPECY-------------------- 59

                          90
                  ....*....|....*
gi 1938929012  87 IRGNTIRQIILPDSL 101
Cdd:cd01723    60 IRGNTIKYLRLPDEV 74
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 7-55 5.24e-05

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: 38.77  E-value: 5.24e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1938929012   7 LKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTDVKLTLPQPRLNKL 55
Cdd:cd00600     1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRVL 49
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 5-42 9.38e-05

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: 38.27  E-value: 9.38e-05
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1938929012   5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTD 42
Cdd:cd01726     4 KFLKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLED 41
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 5-42 7.86e-03

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: 33.34  E-value: 7.86e-03
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1938929012   5 NFLKKLRNEQVTIELKNGTTVWGTLQSVSPQMNAILTD 42
Cdd:cd01722     4 PFLNGLTGKPVIVKLKWGMEYKGTLVSVDSYMNLQLAN 41
 
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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