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Conserved domains on  [gi|119606598|gb|EAW86192|]
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NOL1/NOP2/Sun domain family, member 6, isoform CRA_b [Homo sapiens]

Protein Classification

RsmB/NOP family class I SAM-dependent RNA methyltransferase( domain architecture ID 1000767)

RsmB/NOP family class I SAM-dependent RNA methyltransferase similar to Homo sapiens mitochondrial tRNA (cytosine(34)-C(5))-methyltransferase, which mediates methylation of cytosine to 5-methylcytosine (m5C) at position 34 of mt-tRNA(Met), and to 5-methylcytosine rRNA methyltransferase NSUN4 involved in mitochondrial ribosome small subunit (SSU) maturation by methylation of mitochondrial 12S rRNA

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RsmB super family cl33775
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 14-137 8.60e-20

16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family is part of the Pathway/BioSystem: 16S rRNA modification


The actual alignment was detected with superfamily member COG0144:

Pssm-ID: 439914 [Multi-domain]  Cd Length: 441  Bit Score: 83.90  E-value: 8.60e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598  14 KEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkql 93
Cdd:COG0144  348 EDIAELAALQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL--- 422

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 119606598  94 qrfdpsavpLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 137
Cdd:COG0144  423 ---------LPHRhGTD-------------------GFFIARLRK 439
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 14-137 8.60e-20

16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 439914 [Multi-domain]  Cd Length: 441  Bit Score: 83.90  E-value: 8.60e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598  14 KEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkql 93
Cdd:COG0144  348 EDIAELAALQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL--- 422

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 119606598  94 qrfdpsavpLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 137
Cdd:COG0144  423 ---------LPHRhGTD-------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
14-139 1.04e-16

16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 75.21  E-value: 1.04e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598  14 KEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLkql 93
Cdd:PRK14902 349 EDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQI--- 425

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 119606598  94 qrfdpsavpLPDT-DMDslrearredmlrlankdsiGFFIAKFVKCK 139
Cdd:PRK14902 426 ---------LPNDyGTD-------------------GFFIAKLRKKG 444
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 1-135 3.07e-16

16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA.


Pssm-ID: 426109 [Multi-domain]  Cd Length: 199  Bit Score: 71.69  E-value: 3.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598    1 MGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPqepqIGGEGM 80
Cdd:pfam01189  95 IRRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAVIEYFLQKHPDVELVP----TPLFEP 170

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 119606598   81 RGAGLSCEQLKQLqrfdpsavpLPDTDmdslrearredmlrlaNKDsiGFFIAKF 135
Cdd:pfam01189 171 VGLAIGEQPTLRL---------LPHTH----------------NGD--GFFIAKL 198
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 1-137 9.51e-13

NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 63.25  E-value: 9.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598    1 MGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLqpqEPQIGGEGM 80
Cdd:TIGR00446 156 IRKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF 232

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 119606598   81 rGAGLSCEQLKQLQRFDPSavplpdtdmdslrearredmlrlaNKDSIGFFIAKFVK 137
Cdd:TIGR00446 233 -GINIGKGEVKGALRVFPQ------------------------NYDCEGFFVAKLRK 264
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 14-137 8.60e-20

16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and biogenesis]; 16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 439914 [Multi-domain]  Cd Length: 441  Bit Score: 83.90  E-value: 8.60e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598  14 KEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkql 93
Cdd:COG0144  348 EDIAELAALQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL--- 422

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 119606598  94 qrfdpsavpLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 137
Cdd:COG0144  423 ---------LPHRhGTD-------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
14-139 1.04e-16

16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 75.21  E-value: 1.04e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598  14 KEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLkql 93
Cdd:PRK14902 349 EDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQI--- 425

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 119606598  94 qrfdpsavpLPDT-DMDslrearredmlrlankdsiGFFIAKFVKCK 139
Cdd:PRK14902 426 ---------LPNDyGTD-------------------GFFIAKLRKKG 444
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 1-135 3.07e-16

16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ribosomal methyltransferase RsmB/F enzyme. There is a catalytic cysteine residue at 180 in UniProtKB:Q5SII2, with another highly conserved cysteine at residue 230. It methylates the C(5) position of cytosine 2870 (m5C2870) in 25S rRNA.


Pssm-ID: 426109 [Multi-domain]  Cd Length: 199  Bit Score: 71.69  E-value: 3.07e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598    1 MGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPqepqIGGEGM 80
Cdd:pfam01189  95 IRRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAVIEYFLQKHPDVELVP----TPLFEP 170

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 119606598   81 RGAGLSCEQLKQLqrfdpsavpLPDTDmdslrearredmlrlaNKDsiGFFIAKF 135
Cdd:pfam01189 171 VGLAIGEQPTLRL---------LPHTH----------------NGD--GFFIAKL 198
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 21-75 3.16e-15

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 71.11  E-value: 3.16e-15
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 119606598  21 PLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQI 75
Cdd:PRK14901 361 PLQAELLESLAPLLKPGGTLVYATCTLHPAENEAQIEQFLARHPDWKLEPPKQKI 415
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 1-137 9.51e-13

NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 63.25  E-value: 9.51e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598    1 MGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLqpqEPQIGGEGM 80
Cdd:TIGR00446 156 IRKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF 232

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 119606598   81 rGAGLSCEQLKQLQRFDPSavplpdtdmdslrearredmlrlaNKDSIGFFIAKFVK 137
Cdd:TIGR00446 233 -GINIGKGEVKGALRVFPQ------------------------NYDCEGFFVAKLRK 264
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 11-64 7.58e-12

rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 61.46  E-value: 7.58e-12
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 119606598  11 WSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFP 64
Cdd:PRK11933 209 WSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNREENQAVCLWLKETYP 262
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
16-137 7.69e-11

16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 58.28  E-value: 7.69e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 119606598  16 VASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQ-EPQIGGegmrgaglsceqlKQLq 94
Cdd:PRK10901 344 IAALAALQSEILDALWPLLKPGGTLLYATCSILPEENEQQIKAFLARHPDAELLDTgTPQQPG-------------RQL- 409

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....
gi 119606598  95 rfdpsavpLP-DTDMDslrearredmlrlankdsiGFFIAKFVK 137
Cdd:PRK10901 410 --------LPgEEDGD-------------------GFFYALLIK 426
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 22-70 1.53e-08

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 51.98  E-value: 1.53e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 119606598  22 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQP 70
Cdd:PRK14904 355 LQAELLDHAASLLKPGGVLVYATCSIEPEENELQIEAFLQRHPEFSAEP 403
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 3-77 1.41e-07

16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. The reading frame was originally interpreted as two reading frames, fmu and fmv. The recombinant protein from E. coli was shown to methylate only C967 of small subunit (16S) ribosomal RNA and to produce only m5C at that position. The seed alignment is built from bacterial sequences only. Eukaryotic homologs include Nop2, a protein required for processing pre-rRNA, that is likely also a rRNA methyltransferase, although the fine specificity may differ. Cutoff scores are set to avoid treating archaeal and eukaroytic homologs automatically as functionally equivalent, although they may have very similar roles. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 273141 [Multi-domain]  Cd Length: 426  Bit Score: 49.10  E-value: 1.41e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 119606598    3 QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQL----QPQEPQIGG 77
Cdd:TIGR00563 327 RHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 22-62 2.49e-04

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 39.47  E-value: 2.49e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 119606598  22 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQV-AWALTK 62
Cdd:PRK14903 344 IQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVkRFVYEQ 385
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 24-62 1.00e-03

23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]; 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 37.85  E-value: 1.00e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|.
gi 119606598  24 RKLFTAAVQLLKPEGVLVYSTCT--ITLAENEEQVAWALTK 62
Cdd:COG1092  314 KDLNRLALKLLAPGGILVTSSCSrhFSLDLFLEILARAARD 354
 
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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