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Conserved domains on  [gi|281485631|ref|NP_001099264|]
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N(alpha)-acetyltransferase 38, NatC auxiliary subunit [Rattus norvegicus]

Protein Classification

LSM domain-containing protein( domain architecture ID 10150548)

LSM domain-containing protein similar to U6 snRNA-associated Sm-like LSM domain-containing 1 (LSMD1), which is involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation, and similar to an auxillary component of the N-terminal acetyltransferase C complex, which acetylates N-terminal methionines

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 42-115 8.88e-38

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: 122.28  E-value: 8.88e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281485631  42 RQQLEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPSDsFSAGEPRVLGLAMVPGHHIVSIEVQ 115
Cdd:cd06168    1 RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD-LGAEEPRSLGLVMVPGKHIVSIEVD 73
 
Name Accession Description Interval E-value
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 42-115 8.88e-38

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: 122.28  E-value: 8.88e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281485631  42 RQQLEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPSDsFSAGEPRVLGLAMVPGHHIVSIEVQ 115
Cdd:cd06168    1 RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD-LGAEEPRSLGLVMVPGKHIVSIEVD 73
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 44-114 3.87e-13

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 59.43  E-value: 3.87e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281485631    44 QLEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKpsdsfSAGEPRVLGLAMVPGHHIVSIEV 114
Cdd:smart00651   2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVK-----DGEKKRKLGLVFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 45-114 5.59e-13

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: 59.06  E-value: 5.59e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281485631   45 LEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPsdsfsaGEPRVLGLAMVPGHHIVSIEV 114
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD------GEVRKLGLVLIRGNNIVLISP 66
 
Name Accession Description Interval E-value
LSMD1 cd06168
LSM domain containing 1; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 42-115 8.88e-38

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: 122.28  E-value: 8.88e-38
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 281485631  42 RQQLEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPSDsFSAGEPRVLGLAMVPGHHIVSIEVQ 115
Cdd:cd06168    1 RLKLRKLLGRTLRVTLTDGRVLVGTFVCTDKDGNIILSNAEEYRKPSD-LGAEEPRSLGLVMVPGKHIVSIEVD 73
Sm_B cd01717
Sm protein B; The eukaryotic Sm proteins (B/B', D1, D2, D3, E, F and G) assemble into a ...
 45-115 1.01e-15

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: 66.42  E-value: 1.01e-15
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 281485631  45 LEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPSDSFSAG-----EPRVLGLAMVPGHHIVSIEVQ 115
Cdd:cd01717    5 MLQYINYRMRVTLQDGRQFVGTFLAFDKHMNLVLSDCEEFRKIKPKKKKKgeereEKRVLGLVLLRGENVVSMTVE 80
Sm_like cd00600
Sm and related proteins; The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to ...
 45-113 5.07e-15

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: 64.19  E-value: 5.07e-15
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 281485631  45 LEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPsdsfsaGEPRVLGLAMVPGHHIVSIE 113
Cdd:cd00600    1 LKDFIGKTVSVELKDGRVLTGTLVAFDKYMNLVLDDVVETGRD------GKVRVLGLVLIRGSNIVSIR 63
Sm smart00651
snRNP Sm proteins; small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA ...
 44-114 3.87e-13

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


Pssm-ID: 197820 [Multi-domain]  Cd Length: 67  Bit Score: 59.43  E-value: 3.87e-13
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281485631    44 QLEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKpsdsfSAGEPRVLGLAMVPGHHIVSIEV 114
Cdd:smart00651   2 FLKKLIGKRVLVELKNGREYRGTLKGFDQFMNLVLEDVEETVK-----DGEKKRKLGLVFIRGNNIVYIIL 67
LSM pfam01423
LSM domain; The LSM domain contains Sm proteins as well as other related LSM (Like Sm) ...
 45-114 5.59e-13

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: 59.06  E-value: 5.59e-13
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281485631   45 LEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLKPsdsfsaGEPRVLGLAMVPGHHIVSIEV 114
Cdd:pfam01423   3 LKKLLGKRVLVELKNGRELRGTLKGFDQFMNLVLDDVEETIKD------GEVRKLGLVLIRGNNIVLISP 66
LSm7 cd01729
Like-Sm protein 7; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 45-112 2.83e-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: 39.88  E-value: 2.83e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 281485631  45 LEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEFLK-PSDSFS-AGEPRVLGLAMVPGHHIVSI 112
Cdd:cd01729    7 LSKYVDKKIRVKFQGGREVTGILKGYDQLLNLVLDDTVEYLRdPEDPYKlTDETRSLGLVVCRGTSVVLI 76
LSm8 cd01727
Like-Sm protein 8; The eukaryotic LSm proteins (LSm2-8 or LSm1-7) assemble into a ...
 45-112 5.21e-04

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: 36.35  E-value: 5.21e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 281485631  45 LEALLNKTMRIRMTDGRTLVGCFLCTDRDCNVILGSAQEflkpsDSFSAGEPR---VLGLAMVPGHHIVSI 112
Cdd:cd01727    4 LEDYLNKRVVVITTDGRVIVGTLKGFDQTTNLILSNCHE-----RVYSSDEGVeevPLGLYLLRGDNVAVI 69
Gemin6 cd11676
Gemin 6; Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and ...
 45-115 2.34e-03

Gemin 6; Gemins 6, together with the survival motor neuron (SMN) protein, other Gemins, and Unr-interacting protein (UNRIP) form the SMN complex, which plays an important role in the Sm core assembly reaction, by binding directly to the Sm proteins, as well as UsnRNAs. Gemin 6 forms a heterodimer with Gemin 7, which serve as a surrogate for the SmB-SmD3 dimer during the formation of the heptameric Sm ring.


Pssm-ID: 212487  Cd Length: 63  Bit Score: 34.16  E-value: 2.34e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 281485631  45 LEALLNKTMRIRMTDGRTLVGCFLCTDR-DCNVILGSAQEFLKPSdsfsageprvlgLAMVPGHHIVSIEVQ 115
Cdd:cd11676    4 WKSYVGKEVKVTASDGKTYTGWVYTVDPvSASVVLVQFLEDEKDK------------VKVVMGHAVKSVEVV 63
 
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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