NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|755514245|ref|XP_011239153|]
View 

28S rRNA (cytosine-C(5))-methyltransferase isoform X2 [Mus musculus]

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

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

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 ...
18-347 2.62e-52

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: 180.20  E-value: 2.62e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  18 VRVNTLKTRPEDAIDYFKRQGFSyqgrassvcyVRPClchvpvvskqtfrngsslplcwfKALPQVLRLvyledlralkg 97
Cdd:COG0144  179 LRVNTLKASREELLARLAEEGIE----------AEPT-----------------------PLSPDGLRL----------- 214
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  98 qhflldpllpellvfPAQTDLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFA 177
Cdd:COG0144  215 ---------------EGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVA 279
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 178 FDQDAKRLAAMATLVARAGVSCCELAEKDFLTvsPSDQRYSQVQYILLDPSCSGSGMLSRQleehgegtP------SKER 251
Cdd:COG0144  280 VDISEHRLKRLRENLARLGLSNVEVVVADARE--LLEWLPGKFDRVLLDAPCSGTGTLRRH--------PdikwrrTPED 349
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 252 LQALAGFQQRALCHALRFpsLQ---RLVYSTCSLCQEENEDVVQEALQHNSGtFRLAPVLPTWPHRGLStfpgSEHCLRA 328
Cdd:COG0144  350 IAELAALQRELLDAAARL--LKpggRLVYSTCSLLPEENEEVVEAFLARHPD-FELVPLAELLPGLALT----DGGYLRL 422
                        330
                 ....*....|....*....
gi 755514245 329 SPETTLTGGFFIAVFERAE 347
Cdd:COG0144  423 LPHRHGTDGFFIARLRKKA 441
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
18-347 2.62e-52

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: 180.20  E-value: 2.62e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  18 VRVNTLKTRPEDAIDYFKRQGFSyqgrassvcyVRPClchvpvvskqtfrngsslplcwfKALPQVLRLvyledlralkg 97
Cdd:COG0144  179 LRVNTLKASREELLARLAEEGIE----------AEPT-----------------------PLSPDGLRL----------- 214
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  98 qhflldpllpellvfPAQTDLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFA 177
Cdd:COG0144  215 ---------------EGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVA 279
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 178 FDQDAKRLAAMATLVARAGVSCCELAEKDFLTvsPSDQRYSQVQYILLDPSCSGSGMLSRQleehgegtP------SKER 251
Cdd:COG0144  280 VDISEHRLKRLRENLARLGLSNVEVVVADARE--LLEWLPGKFDRVLLDAPCSGTGTLRRH--------PdikwrrTPED 349
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 252 LQALAGFQQRALCHALRFpsLQ---RLVYSTCSLCQEENEDVVQEALQHNSGtFRLAPVLPTWPHRGLStfpgSEHCLRA 328
Cdd:COG0144  350 IAELAALQRELLDAAARL--LKpggRLVYSTCSLLPEENEEVVEAFLARHPD-FELVPLAELLPGLALT----DGGYLRL 422
                        330
                 ....*....|....*....
gi 755514245 329 SPETTLTGGFFIAVFERAE 347
Cdd:COG0144  423 LPHRHGTDGFFIARLRKKA 441
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
117-314 2.68e-38

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 142.38  E-value: 2.68e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 117 DLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAG 196
Cdd:PRK14901 222 SIRQLPGYEEGWWTVQDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLG 301
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 197 VSCCELAEKDFLTVSP-SDQRYSQVQYILLDPSCSGSGMLSRqleeHGEG--TPSKERLQALAGFQQRALCHALRFPSLQ 273
Cdd:PRK14901 302 LKSIKILAADSRNLLElKPQWRGYFDRILLDAPCSGLGTLHR----HPDArwRQTPEKIQELAPLQAELLESLAPLLKPG 377
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 755514245 274 -RLVYSTCSLCQEENEDVVQEALQHNSgTFRLAPVLPT-WPHR 314
Cdd:PRK14901 378 gTLVYATCTLHPAENEAQIEQFLARHP-DWKLEPPKQKiWPHR 419
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
122-345 7.64e-33

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 123.73  E-value: 7.64e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  122 PLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAGVSCCE 201
Cdd:TIGR00446  46 PEYLFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTI 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  202 LAEKDFLTVSPSDQRYSQvqyILLDPSCSGSGMLSRqlEEHGEGTPSKERLQALAGFQQRALCHAlrFPSLQR---LVYS 278
Cdd:TIGR00446 126 VINADGRKFGAYLLKFDA---ILLDAPCSGEGVIRK--DPSRKRNWSEEDIKYCSLLQKELIDAA--IDALKPggvLVYS 198
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755514245  279 TCSLCQEENEDVVQEALQHNSGTFRLAP--VLPTWPHRGLSTFPGsehCLRASPETTLTGGFFIAVFER 345
Cdd:TIGR00446 199 TCSLEVEENEEVIDYILRKRPDVVEEIIkgDEFFGINIGKGEVKG---ALRVFPQNYDCEGFFVAKLRK 264
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
140-343 2.76e-32

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: 120.22  E-value: 2.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  140 AMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAGVSCCELAEKDfltVSPSDQRYSQ 219
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGD---GRQPDQWLGG 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  220 VQY--ILLDPSCSGSGMLSRQLEEHGEGTPskERLQALAGFQQRALCHALrfPSLQR---LVYSTCSLCQEENEDVVQEA 294
Cdd:pfam01189  78 VLFdrILLDAPCSGTGVIRRHPDVKWLRQE--ADIAQLAQLQKELLSAAI--DLLKPggvLVYSTCSVLPEENEAVIEYF 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 755514245  295 LQ-HNSgtfrlAPVLPTWPHRGLSTFPGSEHCLRASPETTLTGGFFIAVF 343
Cdd:pfam01189 154 LQkHPD-----VELVPTPLFEPVGLAIGEQPTLRLLPHTHNGDGFFIAKL 198
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
18-347 2.62e-52

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: 180.20  E-value: 2.62e-52
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  18 VRVNTLKTRPEDAIDYFKRQGFSyqgrassvcyVRPClchvpvvskqtfrngsslplcwfKALPQVLRLvyledlralkg 97
Cdd:COG0144  179 LRVNTLKASREELLARLAEEGIE----------AEPT-----------------------PLSPDGLRL----------- 214
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  98 qhflldpllpellvfPAQTDLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFA 177
Cdd:COG0144  215 ---------------EGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVA 279
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 178 FDQDAKRLAAMATLVARAGVSCCELAEKDFLTvsPSDQRYSQVQYILLDPSCSGSGMLSRQleehgegtP------SKER 251
Cdd:COG0144  280 VDISEHRLKRLRENLARLGLSNVEVVVADARE--LLEWLPGKFDRVLLDAPCSGTGTLRRH--------PdikwrrTPED 349
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 252 LQALAGFQQRALCHALRFpsLQ---RLVYSTCSLCQEENEDVVQEALQHNSGtFRLAPVLPTWPHRGLStfpgSEHCLRA 328
Cdd:COG0144  350 IAELAALQRELLDAAARL--LKpggRLVYSTCSLLPEENEEVVEAFLARHPD-FELVPLAELLPGLALT----DGGYLRL 422
                        330
                 ....*....|....*....
gi 755514245 329 SPETTLTGGFFIAVFERAE 347
Cdd:COG0144  423 LPHRHGTDGFFIARLRKKA 441
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
117-314 2.68e-38

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 142.38  E-value: 2.68e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 117 DLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAG 196
Cdd:PRK14901 222 SIRQLPGYEEGWWTVQDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLG 301
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 197 VSCCELAEKDFLTVSP-SDQRYSQVQYILLDPSCSGSGMLSRqleeHGEG--TPSKERLQALAGFQQRALCHALRFPSLQ 273
Cdd:PRK14901 302 LKSIKILAADSRNLLElKPQWRGYFDRILLDAPCSGLGTLHR----HPDArwRQTPEKIQELAPLQAELLESLAPLLKPG 377
                        170       180       190       200
                 ....*....|....*....|....*....|....*....|...
gi 755514245 274 -RLVYSTCSLCQEENEDVVQEALQHNSgTFRLAPVLPT-WPHR 314
Cdd:PRK14901 378 gTLVYATCTLHPAENEAQIEQFLARHP-DWKLEPPKQKiWPHR 419
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
18-345 1.96e-35

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 134.92  E-value: 1.96e-35
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  18 VRVNTLKTRPEDAIDYFKRQGFSYqgRASSVCyvrpclchvpvvskqtfrngsslplcwfkalpqvlrlvyLEDLRALKG 97
Cdd:PRK14902 181 IRVNTLKISVEELIEKLEEEGYEV--EESLLS---------------------------------------PEALVIEKG 219
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  98 qhflldpllpellvfpaqtDLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFA 177
Cdd:PRK14902 220 -------------------NIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVA 280
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 178 FD----------QDAKRLaamatlvaraGVSCCELAEKDFLTVspsDQRYSQV-QYILLDPSCSGSGMLSRQleehgegt 246
Cdd:PRK14902 281 LDihehklklieENAKRL----------GLTNIETKALDARKV---HEKFAEKfDKILVDAPCSGLGVIRRK-------- 339
                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 247 P------SKERLQALAGFQQRALCHALrfPSLQ---RLVYSTCSLCQEENEDVVQEALQHNSGtFRLAPVLPTWPhrGLS 317
Cdd:PRK14902 340 PdikynkTKEDIESLQEIQLEILESVA--QYLKkggILVYSTCTIEKEENEEVIEAFLEEHPE-FELVPLQHEKP--DEL 414
                        330       340
                 ....*....|....*....|....*...
gi 755514245 318 TFPGSEHCLRASPETTLTGGFFIAVFER 345
Cdd:PRK14902 415 VYEVKDGYLQILPNDYGTDGFFIAKLRK 442
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
122-345 7.64e-33

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 123.73  E-value: 7.64e-33
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  122 PLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAGVSCCE 201
Cdd:TIGR00446  46 PEYLFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTI 125
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  202 LAEKDFLTVSPSDQRYSQvqyILLDPSCSGSGMLSRqlEEHGEGTPSKERLQALAGFQQRALCHAlrFPSLQR---LVYS 278
Cdd:TIGR00446 126 VINADGRKFGAYLLKFDA---ILLDAPCSGEGVIRK--DPSRKRNWSEEDIKYCSLLQKELIDAA--IDALKPggvLVYS 198
                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 755514245  279 TCSLCQEENEDVVQEALQHNSGTFRLAP--VLPTWPHRGLSTFPGsehCLRASPETTLTGGFFIAVFER 345
Cdd:TIGR00446 199 TCSLEVEENEEVIDYILRKRPDVVEEIIkgDEFFGINIGKGEVKG---ALRVFPQNYDCEGFFVAKLRK 264
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
140-343 2.76e-32

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: 120.22  E-value: 2.76e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  140 AMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAGVSCCELAEKDfltVSPSDQRYSQ 219
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGD---GRQPDQWLGG 77
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  220 VQY--ILLDPSCSGSGMLSRQLEEHGEGTPskERLQALAGFQQRALCHALrfPSLQR---LVYSTCSLCQEENEDVVQEA 294
Cdd:pfam01189  78 VLFdrILLDAPCSGTGVIRRHPDVKWLRQE--ADIAQLAQLQKELLSAAI--DLLKPggvLVYSTCSVLPEENEAVIEYF 153
                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|
gi 755514245  295 LQ-HNSgtfrlAPVLPTWPHRGLSTFPGSEHCLRASPETTLTGGFFIAVF 343
Cdd:pfam01189 154 LQkHPD-----VELVPTPLFEPVGLAIGEQPTLRLLPHTHNGDGFFIAKL 198
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
111-322 1.38e-30

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 121.32  E-value: 1.38e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 111 VFPAQTDLHEhPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMAT 190
Cdd:PRK14904 215 FLSKDFSLFE-PFLKLGLVSVQNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRS 293
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 191 LVARAGVSCCELAEKDFLTVSPSdqrySQVQYILLDPSCSGSGMLSRQLEEHGEGTPskERLQALAGFQQRALCHALRF- 269
Cdd:PRK14904 294 HASALGITIIETIEGDARSFSPE----EQPDAILLDAPCTGTGVLGRRAELRWKLTP--EKLAELVGLQAELLDHAASLl 367
                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 755514245 270 PSLQRLVYSTCSLCQEENEDVVQEALQ--------HNSGTFRLAPVLPTWPHRGLSTFPGS 322
Cdd:PRK14904 368 KPGGVLVYATCSIEPEENELQIEAFLQrhpefsaePSPGSLPEPFHEVAHPKGAILTLPGE 428
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
119-341 1.68e-23

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: 101.10  E-value: 1.68e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  119 HEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKnQGKIFAFDQDAKRLAAMATLVARAGVS 198
Cdd:TIGR00563 210 HALPGFEEGWVTVQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQVVALDIHEHRLKRVYENLKRLGLT 288
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245  199 cCELAEKDfltvspSDQRY-------SQVQYILLDPSCSGSGMLSRQLEEHGEGTPSKerLQALAGFQQrALCHALrFPS 271
Cdd:TIGR00563 289 -IKAETKD------GDGRGpsqwaenEQFDRILLDAPCSATGVIRRHPDIKWLRKPRD--IAELAELQS-EILDAI-WPL 357
                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 755514245  272 LQR---LVYSTCSLCQEENEDVVQEALQ-HNSGTFRLAPVLPTWPHRGLSTFPGSEHclraspettlTGGFFIA 341
Cdd:TIGR00563 358 LKTggtLVYATCSVLPEENSEQIKAFLQeHPDFPFEKTGTPEQVRDGGLQILPHAEE----------GDGFFYA 421
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
126-371 1.27e-18

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 87.27  E-value: 1.27e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 126 AGHLILQDKASCLP--AMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVARAGVSCCELA 203
Cdd:PRK11933  90 SGLFYIQEASSMLPvaALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVALT 169
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 204 EkdFltvspsDQR------YSQVQYILLDPSCSgsgmlsrqleehGEGTPSK----------ERLQALAGfQQRALC--- 264
Cdd:PRK11933 170 H--F------DGRvfgaalPETFDAILLDAPCS------------GEGTVRKdpdalknwspESNLEIAA-TQRELIesa 228
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 265 -HALRfPSlQRLVYSTCSLCQEENEDVVQEALQHNSGTFRLAPvlptwphrgLST-FPGSEHCLraSPETTL-------- 334
Cdd:PRK11933 229 fHALK-PG-GTLVYSTCTLNREENQAVCLWLKETYPDAVEFEP---------LGDlFPGAEKAL--TEEGFLhvfpqiyd 295
                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 755514245 335 TGGFFIAVFERAEVVPTPAPQTDAMDPEPLSQVPKRK 371
Cdd:PRK11933 296 SEGFFVARLRKTASVPRLPAPKYKVGKFPFTPAKDKE 332
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
122-346 1.62e-18

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 86.40  E-value: 1.62e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 122 PLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAAlLKNQGKIFAFDQDAKRLAAMATLVARAGVScCE 201
Cdd:PRK10901 219 PGFAEGWVSVQDAAAQLAATLLAPQNGERVLDACAAPGGKTAHILE-LAPQAQVVALDIDAQRLERVRENLQRLGLK-AT 296
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 202 LAEKDfltVSPSDQRYSQVQY--ILLDPSCSGSGMLSRQleehgegtPS-----KER-LQALAGfQQRALCHALrFPSLQ 273
Cdd:PRK10901 297 VIVGD---ARDPAQWWDGQPFdrILLDAPCSATGVIRRH--------PDikwlrRPEdIAALAA-LQSEILDAL-WPLLK 363
                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 755514245 274 ---RLVYSTCSLCQEENEDVVQEALQHNSGTFRLAPVLPTWPHRGLstFPGSEHClraspettltGGFFIAVFERA 346
Cdd:PRK10901 364 pggTLLYATCSILPEENEQQIKAFLARHPDAELLDTGTPQQPGRQL--LPGEEDG----------DGFFYALLIKR 427
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
115-293 7.32e-15

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 75.68  E-value: 7.32e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 115 QTDLHEHPLYRAGHLILQDKASCLPAMLLSPPPGSHVIDACAAPGNKTSYIAALLKNQGKIFAFDQDAKRLAAMATLVAR 194
Cdd:PRK14903 205 GVNMNDSRVIKDGLATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKR 284
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 755514245 195 AGVSCCELAEKDFLTVSPSDQrySQVQYILLDPSCSGSGMLSRQLEEHGEgtPSKERLQALAGFQQRALCHALRFpsLQR 274
Cdd:PRK14903 285 LKLSSIEIKIADAERLTEYVQ--DTFDRILVDAPCTSLGTARNHPEVLRR--VNKEDFKKLSEIQLRIVSQAWKL--LEK 358
                        170       180
                 ....*....|....*....|..
gi 755514245 275 ---LVYSTCSLCQEENEDVVQE 293
Cdd:PRK14903 359 ggiLLYSTCTVTKEENTEVVKR 380
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH