NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|530432553|ref|XP_005277661|]
View 

28S rRNA (cytosine-C(5))-methyltransferase isoform X1 [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

 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 ...
 119-254 5.79e-21

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: 93.92  E-value: 5.79e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 119 EDLLEVGSRPGPASqlprfVRVNTLKTCSDDVVDYFKRQGFSYQgrasslddlralkgkhflLDPLMPELLVFPAQTDLH 198
Cdd:COG0144  165 EALLAALNEPPPLD-----LRVNTLKASREELLARLAEEGIEAE------------------PTPLSPDGLRLEGPGPVT 221

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 530432553 199 EHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:COG0144  222 ALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRV 277
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 119-254 5.79e-21

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: 93.92  E-value: 5.79e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 119 EDLLEVGSRPGPASqlprfVRVNTLKTCSDDVVDYFKRQGFSYQgrasslddlralkgkhflLDPLMPELLVFPAQTDLH 198
Cdd:COG0144  165 EALLAALNEPPPLD-----LRVNTLKASREELLARLAEEGIEAE------------------PTPLSPDGLRLEGPGPVT 221

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 530432553 199 EHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:COG0144  222 ALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRV 277
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
114-253 9.19e-21

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 93.32  E-value: 9.19e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 114 GVSRNEDLLEVGSRPGPASqlprfVRVNTLKTCSDDVVDYFKRQGFSYqgRASSL--DDLRALKGkhflldplmpellvf 191
Cdd:PRK14902 162 GEEKAEKILESLNEPPKAS-----IRVNTLKISVEELIEKLEEEGYEV--EESLLspEALVIEKG--------------- 219

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530432553 192 paqtDLHEHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGS 253
Cdd:PRK14902 220 ----NIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGK 277
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 135-254 2.90e-11

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: 64.50  E-value: 2.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553  135 PRFVRVNTLKTCSDDVVDYFKRQGFSYQGRASSLDDLRALKGkhflldplmpellvfpaqTDLHEHPLYRAGHLILQDRA 214
Cdd:TIGR00563 165 PMWLRINRTKHSRDEWLALLAEAGMKGFPHDLAPDAVRLETP------------------AAVHALPGFEEGWVTVQDAS 226

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 530432553  215 SCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKnQGSL 254
Cdd:TIGR00563 227 AQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQV 265
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 219-254 1.07e-09

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: 57.43  E-value: 1.07e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 530432553  219 AMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTV 36
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 119-254 5.79e-21

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: 93.92  E-value: 5.79e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 119 EDLLEVGSRPGPASqlprfVRVNTLKTCSDDVVDYFKRQGFSYQgrasslddlralkgkhflLDPLMPELLVFPAQTDLH 198
Cdd:COG0144  165 EALLAALNEPPPLD-----LRVNTLKASREELLARLAEEGIEAE------------------PTPLSPDGLRLEGPGPVT 221

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 530432553 199 EHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:COG0144  222 ALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRV 277
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
114-253 9.19e-21

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 93.32  E-value: 9.19e-21
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 114 GVSRNEDLLEVGSRPGPASqlprfVRVNTLKTCSDDVVDYFKRQGFSYqgRASSL--DDLRALKGkhflldplmpellvf 191
Cdd:PRK14902 162 GEEKAEKILESLNEPPKAS-----IRVNTLKISVEELIEKLEEEGYEV--EESLLspEALVIEKG--------------- 219

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 530432553 192 paqtDLHEHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGS 253
Cdd:PRK14902 220 ----NIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGK 277
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 106-254 1.49e-13

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 71.63  E-value: 1.49e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 106 LARLKVHRGVSRNEDLLEVGSRPgpasqlPRF-VRVNTLKTCSDDVvdyfkrqgfsyqgrasslddLRALKGKHFLLDPL 184
Cdd:PRK14904 156 LERWIARYGEERTEAMLSYNNQA------PLFgFRINRLKTTPEKF--------------------LAAPADASVTFEKS 209

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 185 MPELLVFPAQTDLHEhPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:PRK14904 210 GLPNFFLSKDFSLFE-PFLKLGLVSVQNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQI 278
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 196-252 1.52e-13

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 71.50  E-value: 1.52e-13
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 530432553 196 DLHEHPLYRAGHLILQDRASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQG 252
Cdd:PRK14901 222 SIRQLPGYEEGWWTVQDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQG 278
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 135-254 2.90e-11

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: 64.50  E-value: 2.90e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553  135 PRFVRVNTLKTCSDDVVDYFKRQGFSYQGRASSLDDLRALKGkhflldplmpellvfpaqTDLHEHPLYRAGHLILQDRA 214
Cdd:TIGR00563 165 PMWLRINRTKHSRDEWLALLAEAGMKGFPHDLAPDAVRLETP------------------AAVHALPGFEEGWVTVQDAS 226

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|
gi 530432553  215 SCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKnQGSL 254
Cdd:TIGR00563 227 AQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQV 265
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 219-254 1.07e-09

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: 57.43  E-value: 1.07e-09
                          10        20        30
                  ....*....|....*....|....*....|....*.
gi 530432553  219 AMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTV 36
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 134-254 4.50e-09

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 57.58  E-value: 4.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 134 LPRFVRVNTLKTCSDDVVDYFKRQGfsyqgrasslddLRALKGKHflldplMPELLVFPA-QTDLHEHPLYRAGHLILQD 212
Cdd:PRK14903 162 LPTMLRVNSLAITREEVIKILAEEG------------TEAVPGKH------SPFSLIVRKlGVNMNDSRVIKDGLATVQG 223

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 530432553 213 RASCLPAMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:PRK14903 224 ESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKI 265
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
135-244 3.35e-08

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 54.81  E-value: 3.35e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 135 PRFVRVNTLKTCSDDVVDYFKRQGFSYQGRASSLDDLRalkgkhfLLDPLmpellvfpaqtDLHEHPLYRAGHLILQDRA 214
Cdd:PRK10901 171 PMWLRVNRRHHSRDAYLALLAEAGIEAFPHAVGPDAIR-------LETPV-----------PVHQLPGFAEGWVSVQDAA 232

                         90       100       110
                 ....*....|....*....|....*....|
gi 530432553 215 SCLPAMLLDPPPGSHVIDACAAPGNKTSHL 244
Cdd:PRK10901 233 AQLAATLLAPQNGERVLDACAAPGGKTAHI 262
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 131-254 8.87e-07

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 50.68  E-value: 8.87e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 530432553 131 ASQLP--RFVRVNTLKTCSDDVVDYFKRQGFSY-------QGRASSLDDLRALkgkhflldPLmpellvfpAQTDLHehp 201
Cdd:PRK11933  28 ACQRPlrRSIRVNTLKISVADFLQLMAPYGWTLtpipwceEGFWIERDDEDAL--------PL--------GNTAEH--- 88

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 530432553 202 lyRAGHLILQDRASCLP--AMLLDPPPGSHVIDACAAPGNKTSHLAALLKNQGSL 254
Cdd:PRK11933  89 --LSGLFYIQEASSMLPvaALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAI 141
 
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