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Conserved domains on  [gi|124513718|ref|XP_001350215|]
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small nuclear ribonucleoprotein E, putative [Plasmodium falciparum 3D7]

Protein Classification

small nuclear ribonucleoprotein E( domain architecture ID 10794291)

small nuclear ribonucleoprotein E has an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, and plays a role in pre-mRNA splicing as a core component of the spliceosomal U1, U2, U4 and U5 small nuclear ribonucleoproteins (snRNPs)

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 1-89 5.15e-49

small nuclear ribonucleoprotein; Provisional


:

Pssm-ID: 185472  Cd Length: 89  Bit Score: 149.88  E-value: 5.15e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124513718  1 MATTNKKLQKIMTQPINQIFRFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGD 80
Cdd:PTZ00138  1 MMMTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGD 80


                ....*....
gi 124513718 81 TITLIMEVK 89
Cdd:PTZ00138 81 NITLIMAAK 89
 
Name Accession Description Interval E-value
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 1-89 5.15e-49

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 149.88  E-value: 5.15e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124513718  1 MATTNKKLQKIMTQPINQIFRFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGD 80
Cdd:PTZ00138  1 MMMTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGD 80


                ....*....
gi 124513718 81 TITLIMEVK 89
Cdd:PTZ00138 81 NITLIMAAK 89
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 9-87 6.56e-43

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: 134.22  E-value: 6.56e-43
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124513718  9 QKIMTQPINQIFRFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGDTITLIME 87
Cdd:cd01718   1 QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQN 79
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 21-87 5.79e-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: 55.59  E-value: 5.79e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124513718  21 RFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKeLGKILLKGDTITLIME 87
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRK-LGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 30-87 6.63e-11

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 52.88  E-value: 6.63e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 124513718   30 QIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGDTITLIME 87
Cdd:smart00651 10 RVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
41-85 2.07e-09

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 49.03  E-value: 2.07e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 124513718 41 IEGIILGFDEYMNMVLDQTKEISVKKNTKKeLGKILLKGDTITLI 85
Cdd:COG1958  27 YRGKLKGYDQHMNLVLEDAEEIDDGEVVRK-LGTVVIRGDNVVFI 70
 
Name Accession Description Interval E-value
PTZ00138 PTZ00138
small nuclear ribonucleoprotein; Provisional
 1-89 5.15e-49

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 185472  Cd Length: 89  Bit Score: 149.88  E-value: 5.15e-49
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124513718  1 MATTNKKLQKIMTQPINQIFRFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGD 80
Cdd:PTZ00138  1 MMMTKRKLQKIMTQPINQIFRFFTEKTRVQIWLYDHPNLRIEGKILGFDEYMNMVLDDAEEVYTKKNTRKDLGRILLKGD 80


                ....*....
gi 124513718 81 TITLIMEVK 89
Cdd:PTZ00138 81 NITLIMAAK 89
Sm_E cd01718
Sm protein E; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 9-87 6.56e-43

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: 134.22  E-value: 6.56e-43
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124513718  9 QKIMTQPINQIFRFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGDTITLIME 87
Cdd:cd01718   1 QKVMVQPINLIFRYLQNKSRVQIWLYEQTDMRIEGKIIGFDEYMNLVLDDAEEVHLKTNTRKPLGRILLKGDNITLIQN 79
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 21-87 5.79e-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: 55.59  E-value: 5.79e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124513718  21 RFFTNKTVVQIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKeLGKILLKGDTITLIME 87
Cdd:pfam01423  1 KFLKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKDGEVRK-LGLVLIRGNNIVLISP 66
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 30-87 6.63e-11

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 52.88  E-value: 6.63e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 124513718   30 QIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKELGKILLKGDTITLIME 87
Cdd:smart00651 10 RVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVKDGEKKRKLGLVFIRGNNIVYIIL 67
LSM1 COG1958
Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];
41-85 2.07e-09

Small nuclear ribonucleoprotein (snRNP) homolog [Transcription];


Pssm-ID: 441561  Cd Length: 71  Bit Score: 49.03  E-value: 2.07e-09
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*
gi 124513718 41 IEGIILGFDEYMNMVLDQTKEISVKKNTKKeLGKILLKGDTITLI 85
Cdd:COG1958  27 YRGKLKGYDQHMNLVLEDAEEIDDGEVVRK-LGTVVIRGDNVVFI 70
archaeal_Sm1 cd01731
archaeal Sm protein 1; The archaeal Sm1 proteins: The Sm proteins are conserved in all three ...
 36-85 9.74e-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: 47.18  E-value: 9.74e-09
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|
gi 124513718 36 KPDMRIEGIILGFDEYMNMVLDQTKEIsVKKNTKKELGKILLKGDTITLI 85
Cdd:cd01731  19 KGGKEVRGVLKGFDQHLNLVLENAEEI-IEGESVRKLGTVLVRGDNVVFI 67
LSm5 cd01732
Like-Sm protein 5; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 31-85 2.35e-08

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: 46.47  E-value: 2.35e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 124513718 31 IWLYDKPDMRIEGIILGFDEYMNMVLDQTKEISVKKNTKKE--LGKILLKGDTITLI 85
Cdd:cd01732  16 IWIIMKSDKEFVGTLLGFDDYVNMVLEDVTEYEITPEGRKItkLDQILLNGNNIAML 72
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 30-86 4.20e-08

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: 45.70  E-value: 4.20e-08
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|....*..
gi 124513718 30 QIWLYDKPDMRIEGIILGFDEYMNMVLDQTKEIsVKKNTKKELGKILLKGDTITLIM 86
Cdd:cd00600   8 TVSVELKDGRVLTGTLVAFDKYMNLVLDDVVET-GRDGKVRVLGLVLIRGSNIVSIR 63
Sm_G cd01719
Sm protein G; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 40-85 2.59e-07

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: 43.66  E-value: 2.59e-07
                        10        20        30        40
                ....*....|....*....|....*....|....*....|....*.
gi 124513718 40 RIEGIILGFDEYMNMVLDQTKEIsVKKNTKKELGKILLKGDTITLI 85
Cdd:cd01719  22 KVSGVLRGFDPFMNLVLDDAVEE-VGDGEKTPIGMVVIRGNSIIMI 66
PRK00737 PRK00737
small nuclear ribonucleoprotein; Provisional
 43-85 1.73e-06

small nuclear ribonucleoprotein; Provisional


Pssm-ID: 179104  Cd Length: 72  Bit Score: 41.52  E-value: 1.73e-06
                        10        20        30        40
                ....*....|....*....|....*....|....*....|...
gi 124513718 43 GIILGFDEYMNMVLDQTKEISVKKNTKKeLGKILLKGDTITLI 85
Cdd:PRK00737 29 GELQGYDIHMNLVLDNAEEIQDGEVVRK-LGKVVIRGDNVVYV 70
archaeal_LSm cd11678
archaeal Like-Sm protein; The archaeal Sm-like (LSm): The Sm proteins are conserved in all ...
 15-85 2.29e-04

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: 36.33  E-value: 2.29e-04
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124513718 15 PINQIFRFFTNKTVVQIwlydKPDMR-IEGIILGFDEYMNMVLDQTKEIsVKKNTKKELGKILLKGDTITLI 85
Cdd:cd11678   1 PNKKVKSLVGSRIRVEM----KGDENqLQGRLVAVDDYMNLHLTDTMEC-VGEEKVRSLGTVVLRGNNILLI 67
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 43-85 2.88e-04

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: 36.41  E-value: 2.88e-04
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|.
gi 124513718 43 GIILGFDEYMNMVLDQTKEIS--------VKKNTKKeLGKILLKGDTITLI 85
Cdd:cd01729  27 GILKGYDQLLNLVLDDTVEYLrdpedpykLTDETRS-LGLVVCRGTSVVLI 76
LSm6 cd01726
Like-Sm protein 6; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 43-79 8.93e-04

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: 34.42  E-value: 8.93e-04
                        10        20        30
                ....*....|....*....|....*....|....*..
gi 124513718 43 GIILGFDEYMNMVLDQTKEIsVKKNTKKELGKILLKG 79
Cdd:cd01726  26 GVLACLDGYMNLVLEDTEEY-VDGQLVAKYGDAFIRG 61
LSm3 cd01730
Like-Sm protein 3; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 38-85 4.09e-03

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: 32.97  E-value: 4.09e-03
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|
gi 124513718 38 DMRIEGIILGFDEYMNMVLDQTKEI------------SVKKNTKKELGKILLKGDTITLI 85
Cdd:cd01730  21 DRELRGRLHAYDQHLNMILGDVEETittveideetyeEIYKTTKRNIPMLFVRGDGVILV 80
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 41-82 4.11e-03

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: 32.91  E-value: 4.11e-03
                        10        20        30        40        50
                ....*....|....*....|....*....|....*....|....*....|..
gi 124513718 41 IEGIILGFDEYMNMVLDQTKE---ISVKKNTKKE-------LGKILLKGDTI 82
Cdd:cd01717  23 FVGTFLAFDKHMNLVLSDCEEfrkIKPKKKKKGEereekrvLGLVLLRGENV 74
 
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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