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Conserved domains on  [gi|124805657|ref|XP_001350501|]
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U6 snRNA-associated Sm-like protein LSm7, putative [Plasmodium falciparum 3D7]

Protein Classification

U6 snRNA-associated Sm-like protein LSm7( domain architecture ID 10109606)

U6 snRNA-associated Sm-like protein LSm7 plays 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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 15-103 2.37e-48

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: 148.89  E-value: 2.37e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124805657  15 NKFMTDIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNDSFVVTDKTRSIGLIVARGTSVALITPVE 94
Cdd:cd01729    1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSVVLISPVD 80


                 ....*....
gi 124805657  95 GTQEISNPF 103
Cdd:cd01729   81 GTEEIENPF 89
 
Name Accession Description Interval E-value
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 15-103 2.37e-48

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: 148.89  E-value: 2.37e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124805657  15 NKFMTDIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNDSFVVTDKTRSIGLIVARGTSVALITPVE 94
Cdd:cd01729    1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSVVLISPVD 80


                 ....*....
gi 124805657  95 GTQEISNPF 103
Cdd:cd01729   81 GTEEIENPF 89
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 20-92 7.86e-16

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: 65.99  E-value: 7.86e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124805657   20 DIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPndsfvvtdKTRSIGLIVARGTSVALITP 92
Cdd:pfam01423   2 FLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDG--------EVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 20-92 7.65e-15

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 63.28  E-value: 7.65e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124805657    20 DIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNdsfvvtdKTRSIGLIVARGTSVALITP 92
Cdd:smart00651   2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-------KKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
21-91 9.11e-11

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 52.88  E-value: 9.11e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDpndsfvvtDKTRSIGLIVARGTSVALIT 91
Cdd:COG1958    9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDG--------EVVRKLGTVVIRGDNVVFIS 71
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 21-92 4.14e-08

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 46.15  E-value: 4.14e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNdsfvvtdkTRSIGLIVARGTSVALITP 92
Cdd:PRK00737   9 LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEV--------VRKLGKVVIRGDNVVYVSP 72
 
Name Accession Description Interval E-value
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 15-103 2.37e-48

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: 148.89  E-value: 2.37e-48
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124805657  15 NKFMTDIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNDSFVVTDKTRSIGLIVARGTSVALITPVE 94
Cdd:cd01729    1 KESILDLSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRDPEDPYKLTDETRSLGLVVCRGTSVVLISPVD 80


                 ....*....
gi 124805657  95 GTQEISNPF 103
Cdd:cd01729   81 GTEEIENPF 89
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 20-94 5.89e-16

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: 66.39  E-value: 5.89e-16
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124805657  20 DIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDpndsfvvTDKTRsIGLIVARGTSVALITPVE 94
Cdd:cd01719    4 ELKKYMDKRLSLKLNGNRKVSGVLRGFDPFMNLVLDDAVEEVGD-------GEKTP-IGMVVIRGNSIIMIEALD 70
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 20-92 7.86e-16

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: 65.99  E-value: 7.86e-16
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124805657   20 DIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPndsfvvtdKTRSIGLIVARGTSVALITP 92
Cdd:pfam01423   2 FLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDG--------EVRKLGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 20-92 7.65e-15

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 63.28  E-value: 7.65e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124805657    20 DIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNdsfvvtdKTRSIGLIVARGTSVALITP 92
Cdd:smart00651   2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGE-------KKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
21-91 9.11e-11

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 52.88  E-value: 9.11e-11
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDpndsfvvtDKTRSIGLIVARGTSVALIT 91
Cdd:COG1958    9 LEKSLGKRVLVKLKDGREYRGKLKGYDQHMNLVLEDAEEIDDG--------EVVRKLGTVVIRGDNVVFIS 71
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 21-91 1.71e-09

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: 49.55  E-value: 1.71e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPndsfvvtdKTRSIGLIVARGTSVALIT 91
Cdd:cd00600    1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDG--------KVRVLGLVLIRGSNIVSIR 63
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 23-92 1.78e-09

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: 49.88  E-value: 1.78e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124805657  23 KFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDpndsfvvtDKTRSIGLIVARGTSVALITP 92
Cdd:cd01731    8 ESLNKNVLVKLKGGKEVRGVLKGFDQHLNLVLENAEEIIEG--------ESVRKLGTVLVRGDNVVFISP 69
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 19-91 2.12e-08

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: 47.16  E-value: 2.12e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124805657  19 TDIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEY---IRDPNDSFVVTDKTRSIGLIVARGTSVALIT 91
Cdd:cd01717    3 SKMLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFrkiKPKKKKKGEEREEKRVLGLVLLRGENVVSMT 78
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 21-81 3.09e-08

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: 46.78  E-value: 3.09e-08
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYirdPNDSFVVTDKTRSIGLIV 81
Cdd:cd06168    4 LRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEY---RKPSDLGAEEPRSLGLVM 61
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 21-92 4.14e-08

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 46.15  E-value: 4.14e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNdsfvvtdkTRSIGLIVARGTSVALITP 92
Cdd:PRK00737   9 LNNALNSPVLVRLKGGREFRGELQGYDIHMNLVLDNAEEIQDGEV--------VRKLGKVVIRGDNVVYVSP 72
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 21-92 1.23e-07

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: 1.23e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYI-----RDPNDSFVVTDKTRSIGLIVARGTSVALITP 92
Cdd:cd01730    6 IRLSLDERVYVKLRGDRELRGRLHAYDQHLNMILGDVEETIttveiDEETYEEIYKTTKRNIPMLFVRGDGVILVSP 82
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 21-91 5.28e-07

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: 43.28  E-value: 5.28e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRdpndsfvvTDKTRSIGLIVARGTSVALIT 91
Cdd:cd01726    6 LKKIIGKPVVVKLKNGVEYRGVLACLDGYMNLVLEDTEEYVD--------GQLVAKYGDAFIRGNNVLYIS 68
archaeal_LSm cd11678
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ...
 21-92 9.24e-07

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: 42.88  E-value: 9.24e-07
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124805657  21 IKKFMNQKIRVKFDG-GREVVGTLIGHDAIFNLVLDKTEEYIRDpndsfvvtDKTRSIGLIVARGTSVALITP 92
Cdd:cd11678    5 VKSLVGSRIRVEMKGdENQLQGRLVAVDDYMNLHLTDTMECVGE--------EKVRSLGTVVLRGNNILLIQP 69
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 22-61 1.36e-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: 42.20  E-value: 1.36e-06
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 124805657  22 KKFMN----QKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYI 61
Cdd:cd01722    3 KPFLNgltgKPVIVKLKWGMEYKGTLVSVDSYMNLQLANTEEYI 46
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 18-100 9.59e-06

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: 40.59  E-value: 9.59e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124805657  18 MTDIKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYI---RDPNDSFVvtdktrsIGLIVARGTSVALITPVE 94
Cdd:cd01727    1 SSLLEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHERVyssDEGVEEVP-------LGLYLLRGDNVAVIGEVD 73


                 ....*.
gi 124805657  95 GTQEIS 100
Cdd:cd01727   74 EELDGS 79
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 21-92 3.19e-05

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: 38.76  E-value: 3.19e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124805657  21 IKKFMNQKIRVKFDGGREVVGTLIGHDAIFNLVLDKTEEYIRDPNdsfvvTDKTRSIGLIVARGTSVALITP 92
Cdd:cd01732    8 IDKCIGSKIWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPE-----GRKITKLDQILLNGNNIAMLVP 74
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 8-94 7.34e-04

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 35.86  E-value: 7.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124805657   8 APTPNKDNKFMTD----IKKFMNQKIRVK---FDGGREVV-GTLIGHDAIFNLVLDKTEEYirdpndsFVVTDKTRSIGL 79
Cdd:PTZ00138   2 MMTKRKLQKIMTQpinqIFRFFTEKTRVQiwlYDHPNLRIeGKILGFDEYMNMVLDDAEEV-------YTKKNTRKDLGR 74

                         90
                 ....*....|....*
gi 124805657  80 IVARGTSVALITPVE 94
Cdd:PTZ00138  75 ILLKGDNITLIMAAK 89
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 41-92 1.84e-03

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: 34.45  E-value: 1.84e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 124805657  41 GTLIGHDAIFNLVLDKTEEYirdpndsFVVTDKTRSIGLIVARGTSVALITP 92
Cdd:cd01718   35 GKIIGFDEYMNLVLDDAEEV-------HLKTNTRKPLGRILLKGDNITLIQN 79
 
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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