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Conserved domains on  [gi|30690152|ref|NP_197990|]
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S-adenosyl-L-methionine-dependent methyltransferases superfamily protein [Arabidopsis thaliana]

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 ...
 232-511 7.51e-55

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: 191.76  E-value: 7.51e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 232 PRYVRVNTLKMDVDSAVQELEKH-YTVQKDETVPDLLVLPPGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:COG0144 176 PLDLRVNTLKASREELLARLAEEgIEAEPTPLSPDGLRLEGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLD 255

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 311 ACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDflGLNPKDPSFAKIRAILLDPSCSGSG 390
Cdd:COG0144 256 LCAAPGGKTLHLAELMGNKGRVVAVDISEHRLKRLRENLARLGLSNVEVVVAD--ARELLEWLPGKFDRVLLDAPCSGTG 333

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 391 TI---TDRLDHLLPShsednnmnyDSMRLHKLavfQKKALAHALSFPKVE-RVVYSTCSIYQIENEDVVSSVlpLASSLG 466
Cdd:COG0144 334 TLrrhPDIKWRRTPE---------DIAELAAL---QRELLDAAARLLKPGgRLVYSTCSLLPEENEEVVEAF--LARHPD 399

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 30690152 467 FKLATPFPQWQRRGLPvfagSEHLLRMDPVEDK-EGFFIALFVRAN 511
Cdd:COG0144 400 FELVPLAELLPGLALT----DGGYLRLLPHRHGtDGFFIARLRKKA 441
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 232-511 7.51e-55

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: 191.76  E-value: 7.51e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 232 PRYVRVNTLKMDVDSAVQELEKH-YTVQKDETVPDLLVLPPGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:COG0144 176 PLDLRVNTLKASREELLARLAEEgIEAEPTPLSPDGLRLEGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLD 255

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 311 ACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDflGLNPKDPSFAKIRAILLDPSCSGSG 390
Cdd:COG0144 256 LCAAPGGKTLHLAELMGNKGRVVAVDISEHRLKRLRENLARLGLSNVEVVVAD--ARELLEWLPGKFDRVLLDAPCSGTG 333

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 391 TI---TDRLDHLLPShsednnmnyDSMRLHKLavfQKKALAHALSFPKVE-RVVYSTCSIYQIENEDVVSSVlpLASSLG 466
Cdd:COG0144 334 TLrrhPDIKWRRTPE---------DIAELAAL---QRELLDAAARLLKPGgRLVYSTCSLLPEENEEVVEAF--LARHPD 399

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 30690152 467 FKLATPFPQWQRRGLPvfagSEHLLRMDPVEDK-EGFFIALFVRAN 511
Cdd:COG0144 400 FELVPLAELLPGLALT----DGGYLRLLPHRHGtDGFFIARLRKKA 441
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
234-509 2.66e-43

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 160.34  E-value: 2.66e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  234 YVRVNTLKMDVDSAVQELEK-HYTVQKDETVPDLLVLPpGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLDAC 312
Cdd:PRK14902 180 SIRVNTLKISVEELIEKLEEeGYEVEESLLSPEALVIE-KGNIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDAC 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  313 SAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNPK-DPSFAKiraILLDPSCSGSGT 391
Cdd:PRK14902 259 AAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVHEKfAEKFDK---ILVDAPCSGLGV 335

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  392 ItdrldhllpSHSED---NNMNYDSMRLHKLavfQKKALAHALSFPKVE-RVVYSTCSIYQIENEDVVSSVlpLASSLGF 467
Cdd:PRK14902 336 I---------RRKPDikyNKTKEDIESLQEI---QLEILESVAQYLKKGgILVYSTCTIEKEENEEVIEAF--LEEHPEF 401

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 30690152  468 KLA-TPFPQWQRRGLPVFAGSEHLL----RMDpvedkeGFFIALFVR 509
Cdd:PRK14902 402 ELVpLQHEKPDELVYEVKDGYLQILpndyGTD------GFFIAKLRK 442
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 235-507 3.12e-29

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 116.41  E-value: 3.12e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   235 VRVNTLKMDVDSAVQELEKHYTVQK----DETVPDLLVLPPGSDLHAHRLvanGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:TIGR00446   1 IRVNTLKINVEDLLERLENRGVVLEptceEYFFEVKESPFSIGSTPEYLF---GYYYPQEASSMIPPIALEPREDERVLD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   311 ACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDflglNPKDPSFA-KIRAILLDPSCSGS 389
Cdd:TIGR00446  78 MAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVINAD----GRKFGAYLlKFDAILLDAPCSGE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   390 GTITDRLDHLLPSHSEDNnmnydsmrlHKLAVFQKKALAHALSFPKVERV-VYSTCSIYQIENEDVVSSVLPlasslGFK 468
Cdd:TIGR00446 154 GVIRKDPSRKRNWSEEDI---------KYCSLLQKELIDAAIDALKPGGVlVYSTCSLEVEENEEVIDYILR-----KRP 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 30690152   469 LATPFPQWQRRGLPVFAGSEHL---LRMDP-VEDKEGFFIALF 507
Cdd:TIGR00446 220 DVVEEIIKGDEFFGINIGKGEVkgaLRVFPqNYDCEGFFVAKL 262
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 297-507 7.07e-27

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: 107.89  E-value: 7.07e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   297 AAALQPQAGWEVLDACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDfLGLNPKDPSFAK 376
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGD-GRQPDQWLGGVL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   377 IRAILLDPSCSGSGTItDRLDHLLPSHSEDnnmnyDSMRLHKLavfQKKALAHALSFPKVERV-VYSTCSIYQIENEDVV 455
Cdd:pfam01189  80 FDRILLDAPCSGTGVI-RRHPDVKWLRQEA-----DIAQLAQL---QKELLSAAIDLLKPGGVlVYSTCSVLPEENEAVI 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30690152   456 SSVL---PLASSLgfklatPFPQWQRRGLPVfaGSEHLLRMDP-VEDKEGFFIALF 507
Cdd:pfam01189 151 EYFLqkhPDVELV------PTPLFEPVGLAI--GEQPTLRLLPhTHNGDGFFIAKL 198
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 308-389 2.83e-06

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 46.27  E-value: 2.83e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 308 VLDACSAPGNKTIHLAALmeGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNP-KDPSFAkirAILLDPSC 386
Cdd:cd02440   2 VLDLGCGTGALALALASG--PGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPeADESFD---VIISDPPL 76


                ...
gi 30690152 387 SGS 389
Cdd:cd02440  77 HHL 79
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 232-511 7.51e-55

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: 191.76  E-value: 7.51e-55
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 232 PRYVRVNTLKMDVDSAVQELEKH-YTVQKDETVPDLLVLPPGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:COG0144 176 PLDLRVNTLKASREELLARLAEEgIEAEPTPLSPDGLRLEGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLD 255

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 311 ACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDflGLNPKDPSFAKIRAILLDPSCSGSG 390
Cdd:COG0144 256 LCAAPGGKTLHLAELMGNKGRVVAVDISEHRLKRLRENLARLGLSNVEVVVAD--ARELLEWLPGKFDRVLLDAPCSGTG 333

                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 391 TI---TDRLDHLLPShsednnmnyDSMRLHKLavfQKKALAHALSFPKVE-RVVYSTCSIYQIENEDVVSSVlpLASSLG 466
Cdd:COG0144 334 TLrrhPDIKWRRTPE---------DIAELAAL---QRELLDAAARLLKPGgRLVYSTCSLLPEENEEVVEAF--LARHPD 399

                       250       260       270       280
                ....*....|....*....|....*....|....*....|....*.
gi 30690152 467 FKLATPFPQWQRRGLPvfagSEHLLRMDPVEDK-EGFFIALFVRAN 511
Cdd:COG0144 400 FELVPLAELLPGLALT----DGGYLRLLPHRHGtDGFFIARLRKKA 441
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
234-509 2.66e-43

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 160.34  E-value: 2.66e-43
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  234 YVRVNTLKMDVDSAVQELEK-HYTVQKDETVPDLLVLPpGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLDAC 312
Cdd:PRK14902 180 SIRVNTLKISVEELIEKLEEeGYEVEESLLSPEALVIE-KGNIAGTDLFKDGLITIQDESSMLVAPALDPKGGDTVLDAC 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  313 SAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNPK-DPSFAKiraILLDPSCSGSGT 391
Cdd:PRK14902 259 AAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVHEKfAEKFDK---ILVDAPCSGLGV 335

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  392 ItdrldhllpSHSED---NNMNYDSMRLHKLavfQKKALAHALSFPKVE-RVVYSTCSIYQIENEDVVSSVlpLASSLGF 467
Cdd:PRK14902 336 I---------RRKPDikyNKTKEDIESLQEI---QLEILESVAQYLKKGgILVYSTCTIEKEENEEVIEAF--LEEHPEF 401

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*..
gi 30690152  468 KLA-TPFPQWQRRGLPVFAGSEHLL----RMDpvedkeGFFIALFVR 509
Cdd:PRK14902 402 ELVpLQHEKPDELVYEVKDGYLQILpndyGTD------GFFIAKLRK 442
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 236-511 8.68e-30

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 121.96  E-value: 8.68e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  236 RVNTLKMDVDSAVQELEK-HYTVQKDETVPDLLVL--PPGS--DLHAHrlvANGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:PRK14901 182 RINPLRTSLEEVQAALAEaGITATPIPGLPQGLRLtgNPGSirQLPGY---EEGWWTVQDRSAQLVAPLLDPQPGEVILD 258

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  311 ACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNPKDPSFAKI--RaILLDPSCSG 388
Cdd:PRK14901 259 ACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADSRNLLELKPQWRGYfdR-ILLDAPCSG 337

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  389 SGTITDRLD---HLLPShsednnmnydsmRLHKLAVFQKKALAHALSFPKVE-RVVYSTCSIYQIENEDVVSSVlpLASS 464
Cdd:PRK14901 338 LGTLHRHPDarwRQTPE------------KIQELAPLQAELLESLAPLLKPGgTLVYATCTLHPAENEAQIEQF--LARH 403

                        250       260       270       280
                 ....*....|....*....|....*....|....*....|....*...
gi 30690152  465 LGFKLATPFPQ-WQRRglpvfagsehllrmdpvEDKEGFFIALFVRAN 511
Cdd:PRK14901 404 PDWKLEPPKQKiWPHR-----------------QDGDGFFMAVLRKKS 434
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 235-507 3.12e-29

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 116.41  E-value: 3.12e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   235 VRVNTLKMDVDSAVQELEKHYTVQK----DETVPDLLVLPPGSDLHAHRLvanGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:TIGR00446   1 IRVNTLKINVEDLLERLENRGVVLEptceEYFFEVKESPFSIGSTPEYLF---GYYYPQEASSMIPPIALEPREDERVLD 77

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   311 ACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDflglNPKDPSFA-KIRAILLDPSCSGS 389
Cdd:TIGR00446  78 MAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVINAD----GRKFGAYLlKFDAILLDAPCSGE 153

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   390 GTITDRLDHLLPSHSEDNnmnydsmrlHKLAVFQKKALAHALSFPKVERV-VYSTCSIYQIENEDVVSSVLPlasslGFK 468
Cdd:TIGR00446 154 GVIRKDPSRKRNWSEEDI---------KYCSLLQKELIDAAIDALKPGGVlVYSTCSLEVEENEEVIDYILR-----KRP 219

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|...
gi 30690152   469 LATPFPQWQRRGLPVFAGSEHL---LRMDP-VEDKEGFFIALF 507
Cdd:TIGR00446 220 DVVEEIIKGDEFFGINIGKGEVkgaLRVFPqNYDCEGFFVAKL 262
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 297-507 7.07e-27

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: 107.89  E-value: 7.07e-27
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   297 AAALQPQAGWEVLDACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDfLGLNPKDPSFAK 376
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGD-GRQPDQWLGGVL 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   377 IRAILLDPSCSGSGTItDRLDHLLPSHSEDnnmnyDSMRLHKLavfQKKALAHALSFPKVERV-VYSTCSIYQIENEDVV 455
Cdd:pfam01189  80 FDRILLDAPCSGTGVI-RRHPDVKWLRQEA-----DIAQLAQL---QKELLSAAIDLLKPGGVlVYSTCSVLPEENEAVI 150

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 30690152   456 SSVL---PLASSLgfklatPFPQWQRRGLPVfaGSEHLLRMDP-VEDKEGFFIALF 507
Cdd:pfam01189 151 EYFLqkhPDVELV------PTPLFEPVGLAI--GEQPTLRLLPhTHNGDGFFIAKL 198
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 232-505 1.29e-25

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: 109.57  E-value: 1.29e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   232 PRYVRVNTLKMDVDSAVQEL-EKHYTVQKDETVPDLLVLPPGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLD 310
Cdd:TIGR00563 165 PMWLRINRTKHSRDEWLALLaEAGMKGFPHDLAPDAVRLETPAAVHALPGFEEGWVTVQDASAQWVATWLAPQNEETILD 244

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   311 ACSAPGNKTIHLAALMeGQGKIIACELNEERVKRLEHTIK-LSGASNIEVCHGDFLGLNPKDPSfAKIRAILLDPSCSGS 389
Cdd:TIGR00563 245 ACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKrLGLTIKAETKDGDGRGPSQWAEN-EQFDRILLDAPCSAT 322

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152   390 GTITDRLDhllpshsednnMNY-----DSMRLHKLAVFQKKALAhalsfPKVER---VVYSTCSIYQIENEDVVSSVLPL 461
Cdd:TIGR00563 323 GVIRRHPD-----------IKWlrkprDIAELAELQSEILDAIW-----PLLKTggtLVYATCSVLPEENSEQIKAFLQE 386

                         250       260       270       280
                  ....*....|....*....|....*....|....*....|....
gi 30690152   462 ASSLGFKLATPFPQWQRRGLPVFAGSEHllrmdpvedKEGFFIA 505
Cdd:TIGR00563 387 HPDFPFEKTGTPEQVRDGGLQILPHAEE---------GDGFFYA 421
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 236-452 1.52e-23

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 103.60  E-value: 1.52e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  236 RVNTLKMDVDSAVQELEkHYTVQKDETVPDLLVLPpgSDLHAHR-LVANGRIFLQGKASSMVAAALQPQAGWEVLDACSA 314
Cdd:PRK14904 184 RINRLKTTPEKFLAAPA-DASVTFEKSGLPNFFLS--KDFSLFEpFLKLGLVSVQNPTQALACLLLNPQPGSTVLDLCAA 260

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  315 PGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNPKDPSfakiRAILLDPSCSGSGTITD 394
Cdd:PRK14904 261 PGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARSFSPEEQP----DAILLDAPCTGTGVLGR 336

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 30690152  395 RLDHLLPSHSEDnnmnydsmrLHKLAVFQKKALAHALSFPKVE-RVVYSTCSIYQIENE 452
Cdd:PRK14904 337 RAELRWKLTPEK---------LAELVGLQAELLDHAASLLKPGgVLVYATCSIEPEENE 386
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 233-505 1.67e-23

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 103.83  E-value: 1.67e-23
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  233 RYVRVNTLKMDVDSAVQELE-KHYTVqkdETVP-----------DLLVLPPGSDL-HahrlvangrifLQG-----KASS 294
Cdd:PRK11933  35 RSIRVNTLKISVADFLQLMApYGWTL---TPIPwceegfwierdDEDALPLGNTAeH-----------LSGlfyiqEASS 100

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  295 M--VAAALQPQAGWE-VLDACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGD---FLGLN 368
Cdd:PRK11933 101 MlpVAALFADDNAPQrVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVALTHFDgrvFGAAL 180

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  369 PKdpSFakiRAILLDPSCSGSGTItdRLDHLLPSH-SEDNNMNydsmrlhkLAVFQK---KALAHALsfpKVERV-VYST 443
Cdd:PRK11933 181 PE--TF---DAILLDAPCSGEGTV--RKDPDALKNwSPESNLE--------IAATQReliESAFHAL---KPGGTlVYST 242

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 30690152  444 CSIYQIENEDVVSSVL---PLASSLgFKLATPFPQWQRRGLPvfagsEHLLRMDP-VEDKEGFFIA 505
Cdd:PRK11933 243 CTLNREENQAVCLWLKetyPDAVEF-EPLGDLFPGAEKALTE-----EGFLHVFPqIYDSEGFFVA 302
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
236-510 1.80e-16

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 81.77  E-value: 1.80e-16
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  236 RVNTLKMDVDSAVQELEKH-YTVQKDETVPDLLVLPPGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAGWEVLDACSA 314
Cdd:PRK10901 175 RVNRRHHSRDAYLALLAEAgIEAFPHAVGPDAIRLETPVPVHQLPGFAEGWVSVQDAAAQLAATLLAPQNGERVLDACAA 254

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  315 PGNKTIHLAALmEGQGKIIACELNEERVKRLEHTIKLSGASNiEVCHGDflGLNPK--------DpsfakirAILLDPSC 386
Cdd:PRK10901 255 PGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGD--ARDPAqwwdgqpfD-------RILLDAPC 323

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  387 SGSGTItdrldhllpshsednnmnydsmRLH-------------KLAVFQKKALAHAlsFPKVE---RVVYSTCSIYQIE 450
Cdd:PRK10901 324 SATGVI----------------------RRHpdikwlrrpediaALAALQSEILDAL--WPLLKpggTLLYATCSILPEE 379

                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30690152  451 NEDVVSSVL---PLASSLGFKLATPfPQWQRrgLPvfaGSEHllrMDpvedkeGFFIALFVRA 510
Cdd:PRK10901 380 NEQQIKAFLarhPDAELLDTGTPQQ-PGRQL--LP---GEED---GD------GFFYALLIKR 427
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 232-455 1.10e-14

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 76.45  E-value: 1.10e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  232 PRYVRVNTLKMDVDSAVQELEKHYTvqkdETVP------DLLVLPPGSDLHAHRLVANGRIFLQGKASSMVAAALQPQAG 305
Cdd:PRK14903 163 PTMLRVNSLAITREEVIKILAEEGT----EAVPgkhspfSLIVRKLGVNMNDSRVIKDGLATVQGESSQIVPLLMELEPG 238

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152  306 WEVLDACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNPK-DPSFAKiraILLDP 384
Cdd:PRK14903 239 LRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADAERLTEYvQDTFDR---ILVDA 315

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 30690152  385 SCSGSGTITDRLDHLLPSHSEDnnmnydsmrLHKLAVFQKKALAHALSF-PKVERVVYSTCSIYQIENEDVV 455
Cdd:PRK14903 316 PCTSLGTARNHPEVLRRVNKED---------FKKLSEIQLRIVSQAWKLlEKGGILLYSTCTVTKEENTEVV 378
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 308-389 2.83e-06

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 46.27  E-value: 2.83e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 30690152 308 VLDACSAPGNKTIHLAALmeGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNP-KDPSFAkirAILLDPSC 386
Cdd:cd02440   2 VLDLGCGTGALALALASG--PGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPeADESFD---VIISDPPL 76


                ...
gi 30690152 387 SGS 389
Cdd:cd02440  77 HHL 79
TrmR COG4122
tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; ...
 289-365 1.77e-05

tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; tRNA 5-hydroxyU34 O-methylase TrmR/YrrM is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443298  Cd Length: 173  Bit Score: 45.56  E-value: 1.77e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 30690152 289 QGKASSMVAAALQPQAgweVLDACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSG-ASNIEVCHGDFL 365
Cdd:COG4122   4 QGRLLYLLARLLGAKR---ILEIGTGTGYSTLWLARALPDDGRLTTIEIDPERAAIARENFARAGlADRIRLILGDAL 78
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 308-374 5.15e-05

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 42.17  E-value: 5.15e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 30690152   308 VLDACSAPGNKTIHLAALmeGQGKIIACELNEERVKRLEHTIKLSGAsNIEVCHGDFLGLNPKDPSF 374
Cdd:pfam13649   1 VLDLGCGTGRLTLALARR--GGARVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAEDLPFPDGSF 64
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 296-374 5.89e-05

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 43.44  E-value: 5.89e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 30690152 296 VAAALQPQAGWEVLDACSAPGNKTIHLAALmegQGKIIACELNEERVKRLEHTIKLSGAsNIEVCHGDFLGLNPKDPSF 374
Cdd:COG2226  14 LLAALGLRPGARVLDLGCGTGRLALALAER---GARVTGVDISPEMLELARERAAEAGL-NVEFVVGDAEDLPFPDGSF 88
Ubie_methyltran pfam01209
ubiE/COQ5 methyltransferase family;
302-374 1.92e-03

ubiE/COQ5 methyltransferase family;


Pssm-ID: 395966 [Multi-domain]  Cd Length: 228  Bit Score: 40.12  E-value: 1.92e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 30690152   302 PQAGWEVLDACSAPGNKTIHLAALMEGQGKIIACELNEERVKRLEHTIKLSGASNIEVCHGDFLGLNPKDPSF 374
Cdd:pfam01209  40 VKRGNKFLDVAGGTGDWTFGLSDSAGSSGKVVGLDINENMLKEGEKKAKEEGKYNIEFLQGNAEELPFEDDSF 112
 
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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