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23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH [Bacillus subtilis]

Protein Classification

23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH( domain architecture ID 10003976)

23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH specifically methylates the pseudouridine at position 1915 (m3Psi1915) in 23S rRNA

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
RlmH COG1576
23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]; 23S ...
1-159 2.05e-94

23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]; 23S rRNA pseudoU1915 N3-methylase RlmH is part of the Pathway/BioSystem: 23S rRNA modification


:

Pssm-ID: 441184  Cd Length: 156  Bit Score: 269.99  E-value: 2.05e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:COG1576     1 MKITIIAVGKLKEKWLKEGIEEYAKRLPRYGKLELIEIPDEKRPKNA---DEEQIKEKEGERILAAIPPGAYVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:COG1576    78 KQLTSEEFAEKLEKWRDSGRSDLAFVIGGADGLSPEVRARADLKLSLSKMTFPHQLVRLILAEQLYRAFTILRGHPYHR 156
 
Name Accession Description Interval E-value
RlmH COG1576
23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]; 23S ...
1-159 2.05e-94

23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]; 23S rRNA pseudoU1915 N3-methylase RlmH is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 441184  Cd Length: 156  Bit Score: 269.99  E-value: 2.05e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:COG1576     1 MKITIIAVGKLKEKWLKEGIEEYAKRLPRYGKLELIEIPDEKRPKNA---DEEQIKEKEGERILAAIPPGAYVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:COG1576    78 KQLTSEEFAEKLEKWRDSGRSDLAFVIGGADGLSPEVRARADLKLSLSKMTFPHQLVRLILAEQLYRAFTILRGHPYHR 156
SPOUT_MTase pfam02590
Predicted SPOUT methyltransferase; This family of proteins are predicted to be SPOUT ...
1-158 6.28e-90

Predicted SPOUT methyltransferase; This family of proteins are predicted to be SPOUT methyltransferases.


Pssm-ID: 460606  Cd Length: 155  Bit Score: 258.48  E-value: 6.28e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKapeNLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:pfam02590   1 MKITIIAVGKLKEKYLREGIAEYLKRLSRYCKLEIIEVPDNK---SSKAAEEEQIKEKEGERILAAIPPGDYVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYH 158
Cdd:pfam02590  78 KQLSSEEFAEKLEKWMLSGRSDLVFVIGGSDGLSEEVRARADEKLSLSKMTFPHQLARVILLEQIYRAFTILNGEPYH 155
PRK00103 PRK00103
rRNA large subunit methyltransferase; Provisional
1-159 1.34e-88

rRNA large subunit methyltransferase; Provisional


Pssm-ID: 234634  Cd Length: 157  Bit Score: 255.04  E-value: 1.34e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:PRK00103    1 MKITIIAVGKLKPKWLKDGIAEYLKRFPRYLKLELIEIPDEKRPKNA---DAEQIKAKEGERILAALPKGARVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:PRK00103   78 KQLSSEEFAQELERWRDDGRSDVAFVIGGADGLSPAVKKRADQSLSLSKLTLPHQLVRVLLAEQLYRAWSILAGHPYHR 156
tRNA_RlmH_YbeA TIGR00246
rRNA large subunit m3Psi methyltransferase RlmH; This protein, in the SPOUT methyltransferase ...
2-159 2.39e-86

rRNA large subunit m3Psi methyltransferase RlmH; This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129349  Cd Length: 153  Bit Score: 249.46  E-value: 2.39e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   2 NINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISpDAHVIALAIEGK 81
Cdd:TIGR00246   1 KINLVAVGTKKPKWVKTGFEEYTRRFPKDAPFELIEIPAGKRGKNA---DIKRILDKEGDRILAAIG-KAHVVTLDIPGK 76
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1238243472  82 MKTSEELADTIDKLATYGKSkVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:TIGR00246  77 PWTTPQLADTLEKWKTDGRD-VTLLIGGPEGLSPTCKAAAEQSWSLSKLTLPHPLVRVIVAESLYRAWSITTNHPYHR 153
RlmH-like cd18081
23S-rRNA-pseudouridine1915-N3-methyltransferase RlmH; 23S rRNA (pseudouridine1915-N3) ...
3-159 2.03e-80

23S-rRNA-pseudouridine1915-N3-methyltransferase RlmH; 23S rRNA (pseudouridine1915-N3)-methyltransferase RlmH catalyzes the addition of a methyl group at the N-3 position of pseudouridine Psi1915 in 23S rRNA to form m(3)Psi1915. This family of proteins belongs to the SPOUT methyltransferases. The SPOUT methyltransferase superfamily is 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: 349954  Cd Length: 152  Bit Score: 234.26  E-value: 2.03e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   3 INIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqdmKIIKDKEGDRILSKISPDAHVIALAIEGKM 82
Cdd:cd18081     1 IRIIAVGKLKEKWLKELIEEYLKRLSRYAKLELIELKDEKIPKSI-----EQIKEKEGERILKALPKGDYVIALDERGKQ 75
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1238243472  83 KTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:cd18081    76 LDSEEFAKLLEKWRDSGGSRIVFVIGGADGLSEEVRKRADLLLSLSKLTFPHQLARVVLLEQLYRAFTILNGHPYHK 152
 
Name Accession Description Interval E-value
RlmH COG1576
23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]; 23S ...
1-159 2.05e-94

23S rRNA pseudoU1915 N3-methylase RlmH [Translation, ribosomal structure and biogenesis]; 23S rRNA pseudoU1915 N3-methylase RlmH is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 441184  Cd Length: 156  Bit Score: 269.99  E-value: 2.05e-94
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:COG1576     1 MKITIIAVGKLKEKWLKEGIEEYAKRLPRYGKLELIEIPDEKRPKNA---DEEQIKEKEGERILAAIPPGAYVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:COG1576    78 KQLTSEEFAEKLEKWRDSGRSDLAFVIGGADGLSPEVRARADLKLSLSKMTFPHQLVRLILAEQLYRAFTILRGHPYHR 156
SPOUT_MTase pfam02590
Predicted SPOUT methyltransferase; This family of proteins are predicted to be SPOUT ...
1-158 6.28e-90

Predicted SPOUT methyltransferase; This family of proteins are predicted to be SPOUT methyltransferases.


Pssm-ID: 460606  Cd Length: 155  Bit Score: 258.48  E-value: 6.28e-90
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKapeNLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:pfam02590   1 MKITIIAVGKLKEKYLREGIAEYLKRLSRYCKLEIIEVPDNK---SSKAAEEEQIKEKEGERILAAIPPGDYVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYH 158
Cdd:pfam02590  78 KQLSSEEFAEKLEKWMLSGRSDLVFVIGGSDGLSEEVRARADEKLSLSKMTFPHQLARVILLEQIYRAFTILNGEPYH 155
PRK00103 PRK00103
rRNA large subunit methyltransferase; Provisional
1-159 1.34e-88

rRNA large subunit methyltransferase; Provisional


Pssm-ID: 234634  Cd Length: 157  Bit Score: 255.04  E-value: 1.34e-88
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   1 MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISPDAHVIALAIEG 80
Cdd:PRK00103    1 MKITIIAVGKLKPKWLKDGIAEYLKRFPRYLKLELIEIPDEKRPKNA---DAEQIKAKEGERILAALPKGARVIALDERG 77
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1238243472  81 KMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:PRK00103   78 KQLSSEEFAQELERWRDDGRSDVAFVIGGADGLSPAVKKRADQSLSLSKLTLPHQLVRVLLAEQLYRAWSILAGHPYHR 156
tRNA_RlmH_YbeA TIGR00246
rRNA large subunit m3Psi methyltransferase RlmH; This protein, in the SPOUT methyltransferase ...
2-159 2.39e-86

rRNA large subunit m3Psi methyltransferase RlmH; This protein, in the SPOUT methyltransferase family, previously designated YbeA in E. coli, was shown to be responsible for a further modification, a methylation, to a pseudouridine base in ribosomal large subunit RNA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129349  Cd Length: 153  Bit Score: 249.46  E-value: 2.39e-86
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   2 NINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqDMKIIKDKEGDRILSKISpDAHVIALAIEGK 81
Cdd:TIGR00246   1 KINLVAVGTKKPKWVKTGFEEYTRRFPKDAPFELIEIPAGKRGKNA---DIKRILDKEGDRILAAIG-KAHVVTLDIPGK 76
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1238243472  82 MKTSEELADTIDKLATYGKSkVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:TIGR00246  77 PWTTPQLADTLEKWKTDGRD-VTLLIGGPEGLSPTCKAAAEQSWSLSKLTLPHPLVRVIVAESLYRAWSITTNHPYHR 153
RlmH-like cd18081
23S-rRNA-pseudouridine1915-N3-methyltransferase RlmH; 23S rRNA (pseudouridine1915-N3) ...
3-159 2.03e-80

23S-rRNA-pseudouridine1915-N3-methyltransferase RlmH; 23S rRNA (pseudouridine1915-N3)-methyltransferase RlmH catalyzes the addition of a methyl group at the N-3 position of pseudouridine Psi1915 in 23S rRNA to form m(3)Psi1915. This family of proteins belongs to the SPOUT methyltransferases. The SPOUT methyltransferase superfamily is 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: 349954  Cd Length: 152  Bit Score: 234.26  E-value: 2.03e-80
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1238243472   3 INIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLsdqdmKIIKDKEGDRILSKISPDAHVIALAIEGKM 82
Cdd:cd18081     1 IRIIAVGKLKEKWLKELIEEYLKRLSRYAKLELIELKDEKIPKSI-----EQIKEKEGERILKALPKGDYVIALDERGKQ 75
                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1238243472  83 KTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK 159
Cdd:cd18081    76 LDSEEFAKLLEKWRDSGGSRIVFVIGGADGLSEEVRKRADLLLSLSKLTFPHQLARVVLLEQLYRAFTILNGHPYHK 152
SPOUT_MTase cd07060
SPOUT superfamily of SAM-dependent RNA methyltransferases; The SPOUT (SpoU-TrmD) ...
84-145 3.51e-05

SPOUT superfamily of SAM-dependent RNA methyltransferases; The SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, also known as class IV methyltransferase family, is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. Members of the SPOUT superfamily that have been characterized functionally are involved in post-transcriptional RNA modification by catalyzing methylation of the 2-OH group of ribose, the N-1 atom of guanosine 37 in tRNA, or the N-3 atom of uridine 1498 in 16S rRNA.


Pssm-ID: 349952  Cd Length: 99  Bit Score: 40.50  E-value: 3.51e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1238243472  84 TSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKR-ADEKLSFSKMTFPHQLMRLILVEQI 145
Cdd:cd07060    37 SSEGFAVKISELEISGGSNIAFVIGGEYGGLEESARAlADEPISISSMTLSAELAATILLEQL 99
Lpd COG1249
Dihydrolipoamide dehydrogenase (E3) component of pyruvate/2-oxoglutarate dehydrogenase complex ...
52-92 1.44e-03

Dihydrolipoamide dehydrogenase (E3) component of pyruvate/2-oxoglutarate dehydrogenase complex or glutathione oxidoreductase [Energy production and conversion]; Dihydrolipoamide dehydrogenase (E3) component of pyruvate/2-oxoglutarate dehydrogenase complex or glutathione oxidoreductase is part of the Pathway/BioSystem: Glycine cleavagePyruvate oxidation


Pssm-ID: 440861 [Multi-domain]  Cd Length: 456  Bit Score: 37.76  E-value: 1.44e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1238243472  52 MKIIKDKEGDRIL--SKISPDA----HVIALAIEGKMkTSEELADTI 92
Cdd:COG1249   391 VKLIADAETGRILgaHIVGPHAgeliHEAALAMEMGL-TVEDLADTI 436
Pyr_redox_dim pfam02852
Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; This family includes both ...
52-92 3.42e-03

Pyridine nucleotide-disulphide oxidoreductase, dimerization domain; This family includes both class I and class II oxidoreductases and also NADH oxidases and peroxidases.


Pssm-ID: 427019 [Multi-domain]  Cd Length: 109  Bit Score: 35.22  E-value: 3.42e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1238243472  52 MKIIKDKEGDRIL--SKISPDA----HVIALAIEGKMkTSEELADTI 92
Cdd:pfam02852  51 VKLVADRETGKILgaHIVGPNAgeliQEAALAIKMGA-TVEDLANTI 96
 
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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