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Conserved domains on  [gi|7305109|ref|NP_038564|]
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ribosomal RNA small subunit methyltransferase NEP1 isoform 1 [Mus musculus]

Protein Classification

ribosomal RNA small subunit methyltransferase NEP1( domain architecture ID 13030971)

ribosomal RNA small subunit methyltransferase NEP1 is a S-adenosyl-L-methionine-dependent pseudouridine N(1)-methyltransferase that methylates a pseudouridine in 18S rRNA

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
Nep1-like cd18088
18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1; 18S rRNA (pseudouridine(1248)-N1) ...
43-238 1.49e-119

18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1; 18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1 (also known as EMG1) methylates pseudouridine at position1248 (Psi1248) in 18S rRNA and is required for small subunit (SSU) ribosomal RNA (rRNA) maturation. Mutations on human cause in Bowen-Conradi Syndrome. Nep1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


:

Pssm-ID: 349961  Cd Length: 204  Bit Score: 339.12  E-value: 1.49e-119
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   43 LIVVLEGASLETVKVG----KTYELLNCDRHKSMLLKNGRDPGEVRPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLI 118
Cdd:cd18088   1 LIVVLEEASLELVPVEiwkkPKYELLNSDDHHNAMKKLKRDPKRGRPDIVHQCLLALLDSPLNKAGLLQVYIHTYNNVLI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109  119 EVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKIGTSFSVE--DISDIRELVPSSDPV 196
Cdd:cd18088  81 EVNPQTRIPRTYKRFCGLMVQLLHKGKIRAANGGEKLLKVIKNPLTDHLPEGCRKIGLSEKGElvNPKELVANLPDDEPI 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 7305109  197 VFVVGAFAHGKVSVE--YTEKMVSISNYPLSAALTCAKVTTAFE 238
Cdd:cd18088 161 VFVIGAFAHGDFSEDtsYADEKISISNYPLSAATVCSRICSAFE 204
 
Name Accession Description Interval E-value
Nep1-like cd18088
18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1; 18S rRNA (pseudouridine(1248)-N1) ...
43-238 1.49e-119

18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1; 18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1 (also known as EMG1) methylates pseudouridine at position1248 (Psi1248) in 18S rRNA and is required for small subunit (SSU) ribosomal RNA (rRNA) maturation. Mutations on human cause in Bowen-Conradi Syndrome. Nep1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349961  Cd Length: 204  Bit Score: 339.12  E-value: 1.49e-119
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   43 LIVVLEGASLETVKVG----KTYELLNCDRHKSMLLKNGRDPGEVRPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLI 118
Cdd:cd18088   1 LIVVLEEASLELVPVEiwkkPKYELLNSDDHHNAMKKLKRDPKRGRPDIVHQCLLALLDSPLNKAGLLQVYIHTYNNVLI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109  119 EVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKIGTSFSVE--DISDIRELVPSSDPV 196
Cdd:cd18088  81 EVNPQTRIPRTYKRFCGLMVQLLHKGKIRAANGGEKLLKVIKNPLTDHLPEGCRKIGLSEKGElvNPKELVANLPDDEPI 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 7305109  197 VFVVGAFAHGKVSVE--YTEKMVSISNYPLSAALTCAKVTTAFE 238
Cdd:cd18088 161 VFVIGAFAHGDFSEDtsYADEKISISNYPLSAATVCSRICSAFE 204
EMG1 pfam03587
EMG1/NEP1 methyltransferase; Members of this family are essential for 40S ribosomal biogenesis. ...
45-237 1.42e-108

EMG1/NEP1 methyltransferase; Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases.


Pssm-ID: 460980  Cd Length: 205  Bit Score: 311.40  E-value: 1.42e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109     45 VVLEGASLETVKVG--------KTYELLNCDRHKSMLLKNGRDPGEVRPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNV 116
Cdd:pfam03587   1 VVLEEASLELVPVEirsrrgkkPSYELLDSDDHYHAMKKLKRDPKRGRPDIVHQCLLALLDSPLNKAGLLQVYIHTEDGV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109    117 LIEVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKIGTSFSVEDISDIRELV--PSSD 194
Cdd:pfam03587  81 LIEVNPETRIPRTYKRFAGLMEQLLHKGSIRAVEGEEPLLKVIKNPLTDHLPPGSKKILLSESGEKVVPSELLAalALDE 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 7305109    195 PVVFVVGAFAHGKVSVEYTE--KMVSISNYPLSAALTCAKVTTAF 237
Cdd:pfam03587 161 PVVFVIGAFAHGDFSDDTKKadKKISISNYPLSAATVCSRICSAF 205
PRK04171 PRK04171
16S rRNA (pseudouridine)(914)-N(1))-methyltransferase Nep1;
42-244 1.05e-39

16S rRNA (pseudouridine)(914)-N(1))-methyltransferase Nep1;


Pssm-ID: 235238  Cd Length: 222  Bit Score: 136.56  E-value: 1.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109    42 RLIVVLEGASLETV---------------KVGKTYE--LLNCDRH-KSML-LKNGRDPGevRPDITHQSLLMLMDSPLNR 102
Cdd:PRK04171   1 MLNLVLAESALELVpreiwnhpavvknarRRGKKPEemLLDSSLHyHAMKkLEDKEKRG--RPDIVHISLLVALDSPLNK 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   103 AGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPqkLLKVIKNPVSDhfpvgcmkigtsfSVED 182
Cdd:PRK04171  79 EGKLRVYIHTRDDKVIYVNPETRLPKNYNRFVGLMEQLLKEGRVPPNGEP--LLEIENKSLEE-------------LLEE 143
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 7305109   183 ISDIR--------------ELVPSSDPVVFVVGAFAHGKVSVEY---TEKMVSISNYPLSAALTCAKVTTAFEEVWGVI 244
Cdd:PRK04171 144 IGPDRiillsekgelvkpkELGKENENIAVGIGGFPHGDFSEKVlelAKKKYSIYGEPLTAWTVVCRVIAAYERLLGLL 222
Emg1 COG1756
rRNA pseudouridine-1189 N-methylase Emg1, Nep1/Mra1 family [Translation, ribosomal structure ...
42-244 3.28e-35

rRNA pseudouridine-1189 N-methylase Emg1, Nep1/Mra1 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441362  Cd Length: 224  Bit Score: 124.96  E-value: 3.28e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   42 RLIVVLEGASLETVKvgktYELLNcdrHKSMLL---KNGRDPGEV---------------------RPDITHQSLLMLMD 97
Cdd:COG1756   1 MLKLILAESALELVP----KELWN---HPAVVKnarRRGKRPSEIlldsslhhaamkrlpeaekrgRPDIVHISLLEALE 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   98 SPLNRAGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPqkLLKVIKNPVSDHF-PVGCMKI-- 174
Cdd:COG1756  74 SPLNKEGKLRVYVHTIDDKVIFVGPETRIPKNYNRFVGLMEQLFKEGRVPPNGKP--LLELENMSLSELLeEINPSRVil 151
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7305109  175 ----GTSFSVEDIsdIRElvPSSDPVVFVVGAFAHGKVS---VEYTEKMVSISNYPLSAALTCAKVTTAFEEVWGVI 244
Cdd:COG1756 152 lsekGEKVSPEEI--ASE--ALEENPCVVIGGFPHGDFSestKKKADKVYSIYDEPLEAWTVASRILYAYEKLLGLL 224
 
Name Accession Description Interval E-value
Nep1-like cd18088
18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1; 18S rRNA (pseudouridine(1248)-N1) ...
43-238 1.49e-119

18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1; 18S rRNA (pseudouridine(1248)-N1)-methyltransferase Nep1 (also known as EMG1) methylates pseudouridine at position1248 (Psi1248) in 18S rRNA and is required for small subunit (SSU) ribosomal RNA (rRNA) maturation. Mutations on human cause in Bowen-Conradi Syndrome. Nep1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349961  Cd Length: 204  Bit Score: 339.12  E-value: 1.49e-119
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   43 LIVVLEGASLETVKVG----KTYELLNCDRHKSMLLKNGRDPGEVRPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNVLI 118
Cdd:cd18088   1 LIVVLEEASLELVPVEiwkkPKYELLNSDDHHNAMKKLKRDPKRGRPDIVHQCLLALLDSPLNKAGLLQVYIHTYNNVLI 80
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109  119 EVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKIGTSFSVE--DISDIRELVPSSDPV 196
Cdd:cd18088  81 EVNPQTRIPRTYKRFCGLMVQLLHKGKIRAANGGEKLLKVIKNPLTDHLPEGCRKIGLSEKGElvNPKELVANLPDDEPI 160
                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 7305109  197 VFVVGAFAHGKVSVE--YTEKMVSISNYPLSAALTCAKVTTAFE 238
Cdd:cd18088 161 VFVIGAFAHGDFSEDtsYADEKISISNYPLSAATVCSRICSAFE 204
EMG1 pfam03587
EMG1/NEP1 methyltransferase; Members of this family are essential for 40S ribosomal biogenesis. ...
45-237 1.42e-108

EMG1/NEP1 methyltransferase; Members of this family are essential for 40S ribosomal biogenesis. The structure of EMG1 has revealed that it is a novel member of the superfamily of alpha/beta knot fold methyltransferases.


Pssm-ID: 460980  Cd Length: 205  Bit Score: 311.40  E-value: 1.42e-108
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109     45 VVLEGASLETVKVG--------KTYELLNCDRHKSMLLKNGRDPGEVRPDITHQSLLMLMDSPLNRAGLLQVYIHTQKNV 116
Cdd:pfam03587   1 VVLEEASLELVPVEirsrrgkkPSYELLDSDDHYHAMKKLKRDPKRGRPDIVHQCLLALLDSPLNKAGLLQVYIHTEDGV 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109    117 LIEVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPQKLLKVIKNPVSDHFPVGCMKIGTSFSVEDISDIRELV--PSSD 194
Cdd:pfam03587  81 LIEVNPETRIPRTYKRFAGLMEQLLHKGSIRAVEGEEPLLKVIKNPLTDHLPPGSKKILLSESGEKVVPSELLAalALDE 160
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 7305109    195 PVVFVVGAFAHGKVSVEYTE--KMVSISNYPLSAALTCAKVTTAF 237
Cdd:pfam03587 161 PVVFVIGAFAHGDFSDDTKKadKKISISNYPLSAATVCSRICSAF 205
PRK04171 PRK04171
16S rRNA (pseudouridine)(914)-N(1))-methyltransferase Nep1;
42-244 1.05e-39

16S rRNA (pseudouridine)(914)-N(1))-methyltransferase Nep1;


Pssm-ID: 235238  Cd Length: 222  Bit Score: 136.56  E-value: 1.05e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109    42 RLIVVLEGASLETV---------------KVGKTYE--LLNCDRH-KSML-LKNGRDPGevRPDITHQSLLMLMDSPLNR 102
Cdd:PRK04171   1 MLNLVLAESALELVpreiwnhpavvknarRRGKKPEemLLDSSLHyHAMKkLEDKEKRG--RPDIVHISLLVALDSPLNK 78
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   103 AGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPqkLLKVIKNPVSDhfpvgcmkigtsfSVED 182
Cdd:PRK04171  79 EGKLRVYIHTRDDKVIYVNPETRLPKNYNRFVGLMEQLLKEGRVPPNGEP--LLEIENKSLEE-------------LLEE 143
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 7305109   183 ISDIR--------------ELVPSSDPVVFVVGAFAHGKVSVEY---TEKMVSISNYPLSAALTCAKVTTAFEEVWGVI 244
Cdd:PRK04171 144 IGPDRiillsekgelvkpkELGKENENIAVGIGGFPHGDFSEKVlelAKKKYSIYGEPLTAWTVVCRVIAAYERLLGLL 222
Emg1 COG1756
rRNA pseudouridine-1189 N-methylase Emg1, Nep1/Mra1 family [Translation, ribosomal structure ...
42-244 3.28e-35

rRNA pseudouridine-1189 N-methylase Emg1, Nep1/Mra1 family [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441362  Cd Length: 224  Bit Score: 124.96  E-value: 3.28e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   42 RLIVVLEGASLETVKvgktYELLNcdrHKSMLL---KNGRDPGEV---------------------RPDITHQSLLMLMD 97
Cdd:COG1756   1 MLKLILAESALELVP----KELWN---HPAVVKnarRRGKRPSEIlldsslhhaamkrlpeaekrgRPDIVHISLLEALE 73
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 7305109   98 SPLNRAGLLQVYIHTQKNVLIEVNPQTRIPRTFDRFCGLMVQLLHKLSVRAADGPqkLLKVIKNPVSDHF-PVGCMKI-- 174
Cdd:COG1756  74 SPLNKEGKLRVYVHTIDDKVIFVGPETRIPKNYNRFVGLMEQLFKEGRVPPNGKP--LLELENMSLSELLeEINPSRVil 151
                       170       180       190       200       210       220       230
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 7305109  175 ----GTSFSVEDIsdIRElvPSSDPVVFVVGAFAHGKVS---VEYTEKMVSISNYPLSAALTCAKVTTAFEEVWGVI 244
Cdd:COG1756 152 lsekGEKVSPEEI--ASE--ALEENPCVVIGGFPHGDFSestKKKADKVYSIYDEPLEAWTVASRILYAYEKLLGLL 224
 
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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