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Conserved domains on  [gi|1228972479|ref|XP_022049933|]
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small nuclear ribonucleoprotein E [Acanthochromis polyacanthus]

Protein Classification

small nuclear ribonucleoprotein E( domain architecture ID 10109544)

small nuclear ribonucleoprotein E is part of the eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) which 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

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

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 11-89 4.79e-55

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: 164.65  E-value: 4.79e-55
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1228972479 11 QKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNITLLQS 89
Cdd:cd01718    1 QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQN 79
 
Name Accession Description Interval E-value
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 11-89 4.79e-55

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: 164.65  E-value: 4.79e-55
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1228972479 11 QKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNITLLQS 89
Cdd:cd01718    1 QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQN 79
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 5-87 4.26e-40

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 127.53  E-value: 4.26e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228972479  5 GQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNI 84
Cdd:PTZ00138   3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNI 82


                 ...
gi 1228972479 85 TLL 87
Cdd:PTZ00138  83 TLI 85
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 23-88 5.16e-17

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 68.29  E-value: 5.16e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1228972479  23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNITLLQ 88
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYII 66
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 23-87 1.61e-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: 67.15  E-value: 1.61e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1228972479 23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNITLL 87
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRK-LGLVLIRGNNIVLI 64
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
43-84 2.78e-10

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 51.34  E-value: 2.78e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1228972479 43 IEGCIIGFDEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNI 84
Cdd:COG1958   27 YRGKLKGYDQHMNLVLEDAEEIDDGEVVRK-LGTVVIRGDNV 67
 
Name Accession Description Interval E-value
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 11-89 4.79e-55

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: 164.65  E-value: 4.79e-55
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1228972479 11 QKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNITLLQS 89
Cdd:cd01718    1 QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQN 79
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 5-87 4.26e-40

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 127.53  E-value: 4.26e-40
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228972479  5 GQGQKVQKVMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNI 84
Cdd:PTZ00138   3 MTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGDNI 82


                 ...
gi 1228972479 85 TLL 87
Cdd:PTZ00138  83 TLI 85
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 23-88 5.16e-17

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 68.29  E-value: 5.16e-17
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1228972479  23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKPLGRIMLKGDNITLLQ 88
Cdd:smart00651  1 KFLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYII 66
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 23-87 1.61e-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: 67.15  E-value: 1.61e-16
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1228972479 23 RYLQNRSRIQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNITLL 87
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRK-LGLVLIRGNNIVLI 64
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
43-84 2.78e-10

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 51.34  E-value: 2.78e-10
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 1228972479 43 IEGCIIGFDEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNI 84
Cdd:COG1958   27 YRGKLKGYDQHMNLVLEDAEEIDDGEVVRK-LGTVVIRGDNV 67
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 31-88 4.24e-10

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: 50.71  E-value: 4.24e-10
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 1228972479 31 IQVWLYEQVNMRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNITLLQ 88
Cdd:cd00600    7 KTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRDGKVRV-LGLVLIRGSNIVSIR 63
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 40-86 3.26e-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: 48.34  E-value: 3.26e-09
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1228972479 40 NMRIEGCIIGFDEYMNLVLDDAEEVhMKTKNRKPLGRIMLKGDNITL 86
Cdd:cd01731   21 GKEVRGVLKGFDQHLNLVLENAEEI-IEGESVRKLGTVLVRGDNVVF 66
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 43-87 1.85e-07

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: 44.16  E-value: 1.85e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1228972479 43 IEGCIIGFDEYMNLVLDDAEEVHMKTKNRK--PLGRIMLKGDNITLL 87
Cdd:cd01732   26 FVGTLLGFDDYVNMVLEDVTEYEITPEGRKitKLDQILLNGNNIAML 72
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 45-84 3.78e-07

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 43.45  E-value: 3.78e-07
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|
gi 1228972479 45 GCIIGFDEYMNLVLDDAEEVhMKTKNRKPLGRIMLKGDNI 84
Cdd:PRK00737  29 GELQGYDIHMNLVLDNAEEI-QDGEVVRKLGKVVIRGDNV 67
LSm11_M cd01739
Like-Sm protein 11, middle domain; The eukaryotic Sm and Sm-like (LSm) proteins associate with ...
 21-71 4.24e-07

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: 43.02  E-value: 4.24e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 1228972479 21 IFRYLQNRSRIQVWLYEQVNMR--IEGCIIGFDEYMNLVLDDAEEVHMKTKNR 71
Cdd:cd01739    1 LHRWMRDRTRVKVYIRKAKGIRgsCEGYLVAFDKHWNLALVDVDETWTRRKYK 53
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 40-90 1.41e-06

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: 41.73  E-value: 1.41e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|.
gi 1228972479 40 NMRIEGCIIGFDEYMNLVLDDAEEVhMKTKNRKPLGRIMLKGDNITLLQSV 90
Cdd:cd01719   20 NRKVSGVLRGFDPFMNLVLDDAVEE-VGDGEKTPIGMVVIRGNSIIMIEAL 69
archaeal_LSm cd11678
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ...
 29-88 3.21e-06

archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, their Sm proteins may play a more general role. Archaeal LSm proteins are likely to represent the ancestral Sm domain. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.


Pssm-ID: 212489  Cd Length: 69  Bit Score: 40.95  E-value: 3.21e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1228972479 29 SRIQVWLYEQVNmRIEGCIIGFDEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNITLLQ 88
Cdd:cd11678   11 SRIRVEMKGDEN-QLQGRLVAVDDYMNLHLTDTMECVGEEKVRS-LGTVVLRGNNILLIQ 68
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 51-84 1.39e-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: 39.04  E-value: 1.39e-05
                         10        20        30
                 ....*....|....*....|....*....|....
gi 1228972479 51 DEYMNLVLDDAEEVHMKTKNRKpLGRIMLKGDNI 84
Cdd:cd01726   32 DGYMNLVLEDTEEYVDGQLVAK-YGDAFIRGNNV 64
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 45-87 3.15e-05

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: 38.72  E-value: 3.15e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|
gi 1228972479 45 GCIIGFDEYMNLVLDDAEE-------VHMKTKNRKPLGRIMLKGDNITLL 87
Cdd:cd01729   27 GILKGYDQLLNLVLDDTVEylrdpedPYKLTDETRSLGLVVCRGTSVVLI 76
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 43-84 4.07e-05

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: 38.30  E-value: 4.07e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|..
gi 1228972479 43 IEGCIIGFDEYMNLVLDDAEEV-HMKTKNRKP---------LGRIMLKGDNI 84
Cdd:cd01717   23 FVGTFLAFDKHMNLVLSDCEEFrKIKPKKKKKgeereekrvLGLVLLRGENV 74
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 43-86 1.02e-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: 34.81  E-value: 1.02e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 1228972479 43 IEGCIIGFDEYMNLVLDDAEEVHMKTKN---RKPLGRIMLKGDNITL 86
Cdd:cd01727   22 IVGTLKGFDQTTNLILSNCHERVYSSDEgveEVPLGLYLLRGDNVAV 68
Sm_F cd01722
Sm protein F; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 41-84 6.00e-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: 32.57  E-value: 6.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 1228972479 41 MRIEGCIIGFDEYMNLVLDDAEEVhMKTKNRKPLGRIMLKGDNI 84
Cdd:cd01722   22 MEYKGTLVSVDSYMNLQLANTEEY-IDGKFTGNLGEVLIRCNNV 64
 
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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