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Conserved domains on  [gi|219114260|ref|XP_002176301|]
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predicted protein [Phaeodactylum tricornutum CCAP 1055/1]

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 ...
 81-401 1.66e-44

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: 160.17  E-value: 1.66e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  81 AARALITKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKETKSRPNRVDQFVQAALRIGA 160
Cdd:COG0144    1 AAALAALRAEAAAAAAALALALLLLALLLLDRALAALLLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 161 TQLLFLKVPEHAAVKETVELLRHDPKTTVPESRIKFVNAVLRRISREGDVLLATTDVTQNAS------PWLVKEWQKSWG 234
Cdd:COG0144   81 LLLLPLLAALLLVAAAQLLAARVAVDEAVGPGAAGLVNAVLRRVLREREALLAAADPVERLAvryshpEWLVERLRAAYG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 235 EEATRKIVAlAMEETP----RVLTIKQHPgsqlEKPMGRIKAVAALFEDSEILPQGsVRVntSPPGSIINWPEYSEGSWW 310
Cdd:COG0144  161 PEEAEALLA-ALNEPPpldlRVNTLKASR----EELLARLAEEGIEAEPTPLSPDG-LRL--EGPGPVTALPGFREGLFS 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 311 LQDAAATTPAIALyNAlsKNGETsvagldVVDMCASPGGKTAQL--WNYGFASVTAVEVAEKRTERLRQNMQRLNMDC-E 387
Cdd:COG0144  233 VQDEASQLVALLL-DP--KPGER------VLDLCAAPGGKTLHLaeLMGNKGRVVAVDISEHRLKRLRENLARLGLSNvE 303

                        330
                 ....*....|....
gi 219114260 388 VVVADGAQWTSQHE 401
Cdd:COG0144  304 VVVADARELLEWLP 317
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 81-401 1.66e-44

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: 160.17  E-value: 1.66e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  81 AARALITKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKETKSRPNRVDQFVQAALRIGA 160
Cdd:COG0144    1 AAALAALRAEAAAAAAALALALLLLALLLLDRALAALLLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 161 TQLLFLKVPEHAAVKETVELLRHDPKTTVPESRIKFVNAVLRRISREGDVLLATTDVTQNAS------PWLVKEWQKSWG 234
Cdd:COG0144   81 LLLLPLLAALLLVAAAQLLAARVAVDEAVGPGAAGLVNAVLRRVLREREALLAAADPVERLAvryshpEWLVERLRAAYG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 235 EEATRKIVAlAMEETP----RVLTIKQHPgsqlEKPMGRIKAVAALFEDSEILPQGsVRVntSPPGSIINWPEYSEGSWW 310
Cdd:COG0144  161 PEEAEALLA-ALNEPPpldlRVNTLKASR----EELLARLAEEGIEAEPTPLSPDG-LRL--EGPGPVTALPGFREGLFS 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 311 LQDAAATTPAIALyNAlsKNGETsvagldVVDMCASPGGKTAQL--WNYGFASVTAVEVAEKRTERLRQNMQRLNMDC-E 387
Cdd:COG0144  233 VQDEASQLVALLL-DP--KPGER------VLDLCAAPGGKTLHLaeLMGNKGRVVAVDISEHRLKRLRENLARLGLSNvE 303

                        330
                 ....*....|....
gi 219114260 388 VVVADGAQWTSQHE 401
Cdd:COG0144  304 VVVADARELLEWLP 317
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
76-388 8.70e-38

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 141.85  E-value: 8.70e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALITKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKetksRPNRVDQFVQAA 155
Cdd:PRK14902   4 NARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIK----KRKKLDPWVRNL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 156 LRIGATQLLFL-KVPEHAAVKETVELlrhdPKTTVPESRIKFVNAVLRRISREGDVLLAT-TDVTQNAS------PWLVK 227
Cdd:PRK14902  80 LRMSLYQLLYLdKVPDHAAVNEAVEI----AKKRGHKGIAKFVNGVLRNILREGLPDIDEiKDPVKRLSikyshpVWLVK 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 228 EWQKSWGEEATRKIVALAMEETP---RVLTIKqhpgSQLEKPMGRIKAVAALFEDSEILPQGsVRVNTsppGSIINWPEY 304
Cdd:PRK14902 156 RWIDQYGEEKAEKILESLNEPPKasiRVNTLK----ISVEELIEKLEEEGYEVEESLLSPEA-LVIEK---GNIAGTDLF 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 305 SEGSWWLQDAAATTPAIALynALsKNGETsvagldVVDMCASPGGKTAQ----LWNYGfaSVTAVEVAEKRTERLRQNMQ 380
Cdd:PRK14902 228 KDGLITIQDESSMLVAPAL--DP-KGGDT------VLDACAAPGGKTTHiaelLKNTG--KVVALDIHEHKLKLIEENAK 296

                        330
                 ....*....|.
gi 219114260 381 RL---NMDCEV 388
Cdd:PRK14902 297 RLgltNIETKA 307
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 75-206 3.72e-25

NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.


Pssm-ID: 460031 [Multi-domain]  Cd Length: 133  Bit Score: 99.65  E-value: 3.72e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260   75 RNARFLAARAL--ITKTGSAAFAVDR----LESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCqkeTKSRP-NR 147
Cdd:pfam01029   1 RNARELALQALyqVEINGSDEEEKGAylneALDKALEGDLSEEDRAFATELVYGVLRNLEELDALIEKL---LENWPlER 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  148 VDQFVQAALRIGATQLLFL-KVPEHAAVKETVELLrhdpKTTVPESRIKFVNAVLRRISR 206
Cdd:pfam01029  78 LSPVDRAILRLGLYELLFLdDVPPHVAINEAVELA----KKFGGEKSAKFVNGVLRNVAR 133
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 75-208 4.66e-19

N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.


Pssm-ID: 238343 [Multi-domain]  Cd Length: 126  Bit Score: 82.39  E-value: 4.66e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  75 RNARFLAARALITKTGSAAFAVDRLESNKHySTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKetksRPNR-VDQFVQ 153
Cdd:cd00620    1 MNARSTAAEVLRDVLQRGASLNAVLSALQK-KDKSDRDRGLATELVYGTLRWLALLDWIINPLLK----KPDVgKDPDVR 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 219114260 154 AALRIGATQLLFLKVPEHAAVKETVELLRHDPKTTVPesriKFVNAVLRRISREG 208
Cdd:cd00620   76 NLLRLGLYQLLYLDVPPHAAVDETVEIAKIRKDLGRA----GLVNAVLRRFERED 126
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 251-393 5.92e-11

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 62.48  E-value: 5.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  251 RVLTIKQHPGSQLEKPMGRIKAVAALFEDseilpqGSVRVNTSPPgSIINWPEYSEGSWWLQDAAATTPAIALYnalSKN 330
Cdd:TIGR00446   2 RVNTLKINVEDLLERLENRGVVLEPTCEE------YFFEVKESPF-SIGSTPEYLFGYYYPQEASSMIPPIALE---PRE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 219114260  331 GETsvagldVVDMCASPGGKTAQLW----NYGfaSVTAVEVAEKRTERLRQNMQRLN-MDCEVVVADG 393
Cdd:TIGR00446  72 DER------VLDMAAAPGGKTTQISqlmkNKG--CIVANEISKSRTKALISNINRMGvLNTIVINADG 131
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 81-401 1.66e-44

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: 160.17  E-value: 1.66e-44
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  81 AARALITKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKETKSRPNRVDQFVQAALRIGA 160
Cdd:COG0144    1 AAALAALRAEAAAAAAALALALLLLALLLLDRALAALLLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 161 TQLLFLKVPEHAAVKETVELLRHDPKTTVPESRIKFVNAVLRRISREGDVLLATTDVTQNAS------PWLVKEWQKSWG 234
Cdd:COG0144   81 LLLLPLLAALLLVAAAQLLAARVAVDEAVGPGAAGLVNAVLRRVLREREALLAAADPVERLAvryshpEWLVERLRAAYG 160

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 235 EEATRKIVAlAMEETP----RVLTIKQHPgsqlEKPMGRIKAVAALFEDSEILPQGsVRVntSPPGSIINWPEYSEGSWW 310
Cdd:COG0144  161 PEEAEALLA-ALNEPPpldlRVNTLKASR----EELLARLAEEGIEAEPTPLSPDG-LRL--EGPGPVTALPGFREGLFS 232

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 311 LQDAAATTPAIALyNAlsKNGETsvagldVVDMCASPGGKTAQL--WNYGFASVTAVEVAEKRTERLRQNMQRLNMDC-E 387
Cdd:COG0144  233 VQDEASQLVALLL-DP--KPGER------VLDLCAAPGGKTLHLaeLMGNKGRVVAVDISEHRLKRLRENLARLGLSNvE 303

                        330
                 ....*....|....
gi 219114260 388 VVVADGAQWTSQHE 401
Cdd:COG0144  304 VVVADARELLEWLP 317
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
76-388 8.70e-38

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 141.85  E-value: 8.70e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALITKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKetksRPNRVDQFVQAA 155
Cdd:PRK14902   4 NARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIK----KRKKLDPWVRNL 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 156 LRIGATQLLFL-KVPEHAAVKETVELlrhdPKTTVPESRIKFVNAVLRRISREGDVLLAT-TDVTQNAS------PWLVK 227
Cdd:PRK14902  80 LRMSLYQLLYLdKVPDHAAVNEAVEI----AKKRGHKGIAKFVNGVLRNILREGLPDIDEiKDPVKRLSikyshpVWLVK 155

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 228 EWQKSWGEEATRKIVALAMEETP---RVLTIKqhpgSQLEKPMGRIKAVAALFEDSEILPQGsVRVNTsppGSIINWPEY 304
Cdd:PRK14902 156 RWIDQYGEEKAEKILESLNEPPKasiRVNTLK----ISVEELIEKLEEEGYEVEESLLSPEA-LVIEK---GNIAGTDLF 227

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 305 SEGSWWLQDAAATTPAIALynALsKNGETsvagldVVDMCASPGGKTAQ----LWNYGfaSVTAVEVAEKRTERLRQNMQ 380
Cdd:PRK14902 228 KDGLITIQDESSMLVAPAL--DP-KGGDT------VLDACAAPGGKTTHiaelLKNTG--KVVALDIHEHKLKLIEENAK 296

                        330
                 ....*....|.
gi 219114260 381 RL---NMDCEV 388
Cdd:PRK14902 297 RLgltNIETKA 307
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
76-396 9.77e-38

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 141.48  E-value: 9.77e-38
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALIT-----KTGSAAFAvdrlesnKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQC-QKETKSRpnrvD 149
Cdd:PRK10901   3 NLRALAAAAILQvvdqgQSLSAALP-------ALQQKVSDKDRALLQELCYGVLRRLPRLEWLIAQLlAKPLKGK----Q 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 150 QFVQAALRIGATQLLFLKVPEHAAVKETVELLRhDPKTtvpESRIKFVNAVLRRISREGDVLLATTDVTQNAS----PWL 225
Cdd:PRK10901  72 RIVHALLLVGLYQLLYTRIPAHAAVDETVEAAK-ALKR---PWAKGLVNAVLRRFQREQEELLAELQADPVARynhpSWL 147

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 226 VKEWQKSWGEEAtRKIVAlAMEETP----RVLTIKQHPGSQLE--KPMGrIKAVA-ALFEDSEILPQgSVRVnTSPPGsi 298
Cdd:PRK10901 148 IKRLKKAYPEQW-QAILA-ANNQRPpmwlRVNRRHHSRDAYLAllAEAG-IEAFPhAVGPDAIRLET-PVPV-HQLPG-- 220

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 299 inwpeYSEGSWWLQDAAATTPAIALynaLSKNGETsvagldVVDMCASPGGKTAQLWNY-GFASVTAVEVAEKRTERLRQ 377
Cdd:PRK10901 221 -----FAEGWVSVQDAAAQLAATLL---APQNGER------VLDACAAPGGKTAHILELaPQAQVVALDIDAQRLERVRE 286

                        330       340
                 ....*....|....*....|..
gi 219114260 378 NMQRLNMDCEVVVADGA---QW 396
Cdd:PRK10901 287 NLQRLGLKATVIVGDARdpaQW 308
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 76-395 7.55e-30

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 119.65  E-value: 7.55e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALiTKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQ-CQKETKSRPNRVdqfvQA 154
Cdd:PRK14901   2 NARQLAWEIL-QAVARGAYADVALERVLRKYPLSGADRALVTELVYGCIRRRRTLDAWIDQlGKKPAHKQPPDL----RW 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 155 ALRIGATQLLFL-KVPEHAAVKETVELlrhdPKTTVPESRIKFVNAVLR---RISREGDVLLATTDVTQNAS-----P-W 224
Cdd:PRK14901  77 LLHLGLYQLRYMdRIPASAAVNTTVEL----AKQNGLGGLAGVVNGILRqylRAREAGDPLPLPEDPIERLAilhsfPdW 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 225 LVKEWQKSWGEEATRKIvALAMEETP----RVLTIKQHPgsqlekpmgriKAVAALFEDSEI-------LPQGsVRVnTS 293
Cdd:PRK14901 153 LVKLWLEWLGLEEAEQL-CKWFNQPPsldlRINPLRTSL-----------EEVQAALAEAGItatpipgLPQG-LRL-TG 218

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 294 PPGSIINWPEYSEGSWWLQDAAA--TTPaiaLYNAlsKNGETsvagldVVDMCASPGGKT---AQLWNyGFASVTAVEVA 368
Cdd:PRK14901 219 NPGSIRQLPGYEEGWWTVQDRSAqlVAP---LLDP--QPGEV------ILDACAAPGGKTthiAELMG-DQGEIWAVDRS 286

                        330       340
                 ....*....|....*....|....*...
gi 219114260 369 EKRTERLRQNMQRLNMDC-EVVVADGAQ 395
Cdd:PRK14901 287 ASRLKKLQENAQRLGLKSiKILAADSRN 314
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 76-385 5.32e-26

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 108.99  E-value: 5.32e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALITKTGSAAFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQC--QKETKSRPnrvdqFVQ 153
Cdd:PRK14904   3 TARELALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFyhHDLEKAAP-----VLK 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 154 AALRIGATQLLFL-KVPEHAAVKETVELLRHDPKttvpESRIKFVNAVLRRISREgdvLLATTDVTQNASP--------- 223
Cdd:PRK14904  78 NILRLGVYQLLFLdRVPRWAAVNECVKLARKYKG----EHMAKLVNGVLRNISPE---TISLDEWLKGMPEaerlsllys 150

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 224 ---WLVKEWQKSWGEEATRKIVAlAMEETP----RVLTIKQHPGSQLEKPmgriKAVAALFEDSEIlpqgsvrvntsppg 296
Cdd:PRK14904 151 hpeWLLERWIARYGEERTEAMLS-YNNQAPlfgfRINRLKTTPEKFLAAP----ADASVTFEKSGL-------------- 211

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 297 siinwpeyseGSWWL-QDAAATTPAIalynalsKNGETSVA---------------GLDVVDMCASPGGKT---AQLW-N 356
Cdd:PRK14904 212 ----------PNFFLsKDFSLFEPFL-------KLGLVSVQnptqalaclllnpqpGSTVLDLCAAPGGKStfmAELMqN 274

                        330       340
                 ....*....|....*....|....*....
gi 219114260 357 YGfaSVTAVEVAEKRTERLRQNMQRLNMD 385
Cdd:PRK14904 275 RG--QITAVDRYPQKLEKIRSHASALGIT 301
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 75-206 3.72e-25

NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by transcriptional antitermination.


Pssm-ID: 460031 [Multi-domain]  Cd Length: 133  Bit Score: 99.65  E-value: 3.72e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260   75 RNARFLAARAL--ITKTGSAAFAVDR----LESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCqkeTKSRP-NR 147
Cdd:pfam01029   1 RNARELALQALyqVEINGSDEEEKGAylneALDKALEGDLSEEDRAFATELVYGVLRNLEELDALIEKL---LENWPlER 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  148 VDQFVQAALRIGATQLLFL-KVPEHAAVKETVELLrhdpKTTVPESRIKFVNAVLRRISR 206
Cdd:pfam01029  78 LSPVDRAILRLGLYELLFLdDVPPHVAINEAVELA----KKFGGEKSAKFVNGVLRNVAR 133
NusB COG0781
Transcription antitermination protein NusB [Transcription];
93-207 3.04e-20

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 85.97  E-value: 3.04e-20
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  93 AFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCqkeTKSRP-NRVDQFVQAALRIGATQLLFL-KVPE 170
Cdd:COG0781   15 AYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPY---LKDWPlERLDPVDRAILRLAAYELLYLdDVPY 91

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 219114260 171 HAAVKETVELLRH--DPKTTvpesriKFVNAVLRRISRE 207
Cdd:COG0781   92 KVAINEAVELAKKfgTEDSP------KFVNGVLDKIAKE 124
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 75-208 4.66e-19

N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine transferase Sun, also known as RrmB or Fmu shares the RNA-binding non-catalytic domain with the transcription termination factor NusB. The precise biological role of this domain in Sun is unknown, although it is likely to be involved in sequence-specific RNA binding. The C-terminal methyltransferase domain of Sun has been shown to catalyze formation of m5C at position 967 of 16S rRNA in Escherichia coli.


Pssm-ID: 238343 [Multi-domain]  Cd Length: 126  Bit Score: 82.39  E-value: 4.66e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  75 RNARFLAARALITKTGSAAFAVDRLESNKHySTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKetksRPNR-VDQFVQ 153
Cdd:cd00620    1 MNARSTAAEVLRDVLQRGASLNAVLSALQK-KDKSDRDRGLATELVYGTLRWLALLDWIINPLLK----KPDVgKDPDVR 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 219114260 154 AALRIGATQLLFLKVPEHAAVKETVELLRHDPKTTVPesriKFVNAVLRRISREG 208
Cdd:cd00620   76 NLLRLGLYQLLYLDVPPHAAVDETVEIAKIRKDLGRA----GLVNAVLRRFERED 126
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 76-207 1.64e-15

RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or Fmu) proteins. This family includes two orthologous groups exemplified by the transcription termination factor NusB and the N-terminal domain of the rRNA-specific 5-methylcytidine transferase (m5C-methyltransferase) Sun. The NusB protein plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation. The m5C-methyltransferase Sun shares the N-terminal non-catalytic RNA-binding domain with NusB.


Pssm-ID: 238253 [Multi-domain]  Cd Length: 129  Bit Score: 72.77  E-value: 1.64e-15
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALI---TKTGSAAFAVDRLESNKhysTLSTRDRSFARLLVTTTERRLGQIDEVLRQcqKETKSRPNRVDQFV 152
Cdd:cd00447    1 SAREIAFQALYqveIRNGISLEAVLSALEKL---QLAKKDRPFALELVYGVLRNLPELDDIISP--LLKKWLLDRLDKVD 75

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 219114260 153 QAALRIGATQLLFLK--VPEHAAVKETVELLRHDPKttvpESRIKFVNAVLRRISRE 207
Cdd:cd00447   76 RAILRLLLYELYQLLydVPPPVAINEAVELAKRFGD----DDSAKFVNGVLRRIAKE 128
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 76-384 1.44e-14

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 74.91  E-value: 1.44e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  76 NARFLAARALITKTGSAAfaVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKETKSRPNrvdqfVQAA 155
Cdd:PRK14903   4 NVRLLAYRLLRKYEKEKF--IFREDVDSVLSFLDDKDRRFFKELVWGVVRKEELLDWYINQLLKKKDIPPA-----VRVA 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 156 LRIGATQLLFL-KVPEHAAVKETVELLRHdpkttvpESRIKFVNAVLRRISRegdvLLATTDVTQNAS--PWLVKEWQKS 232
Cdd:PRK14903  77 LRMGAYQLLFMnSVPDYAAVSETVKLVKN-------ENFKKLVNAVLRRLRT----VPEPKELHLKYShpKWLVNYWRSF 145

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 233 WGEEATRKIVALAMEETPRVLTIKQHPGSQLEkpmgRIKAVAALFEDSEILPQGSV-----RVNTSPPGSiinwPEYSEG 307
Cdd:PRK14903 146 LPEEAVLRIMEWNQEPLPTMLRVNSLAITREE----VIKILAEEGTEAVPGKHSPFslivrKLGVNMNDS----RVIKDG 217

                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 219114260 308 SWWLQdaAATTPAIALYNALSKNgetsvagLDVVDMCASPGGKTAQLWNYGFASVT--AVEVAEKRTERLRQNMQRLNM 384
Cdd:PRK14903 218 LATVQ--GESSQIVPLLMELEPG-------LRVLDTCAAPGGKTTAIAELMKDQGKilAVDISREKIQLVEKHAKRLKL 287
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 251-393 5.92e-11

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 62.48  E-value: 5.92e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  251 RVLTIKQHPGSQLEKPMGRIKAVAALFEDseilpqGSVRVNTSPPgSIINWPEYSEGSWWLQDAAATTPAIALYnalSKN 330
Cdd:TIGR00446   2 RVNTLKINVEDLLERLENRGVVLEPTCEE------YFFEVKESPF-SIGSTPEYLFGYYYPQEASSMIPPIALE---PRE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 219114260  331 GETsvagldVVDMCASPGGKTAQLW----NYGfaSVTAVEVAEKRTERLRQNMQRLN-MDCEVVVADG 393
Cdd:TIGR00446  72 DER------VLDMAAAPGGKTTQISqlmkNKG--CIVANEISKSRTKALISNINRMGvLNTIVINADG 131
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 75-207 8.72e-11

Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key role in the regulation of ribosomal RNA biosynthesis in eubacteria by modulating the efficiency of transcriptional antitermination. NusB along with other Nus factors (NusA, NusE/S10 and NusG) forms the core complex with the boxA element of the nut site of the rRNA operons. These interactions help RNA polymerase to counteract polarity during transcription of rRNA operons and allow stable antitermination. The transcription antitermination system can be appropriated by some bacteriophages such as lambda, which use the system to switch between the lysogenic and lytic modes of phage propagation.


Pssm-ID: 238342 [Multi-domain]  Cd Length: 130  Bit Score: 59.22  E-value: 8.72e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  75 RNARFLAARALITKTGSAAFAVDRLESNKHYSTLstrDRSFARLLVTTTERRLGQIDEVLRQCQKETKSrpNRVDQFVQA 154
Cdd:cd00619    5 RELAVQALYAWELAPEILAEVVSLLELLQYKSKK---VLPFALKLVRGVLENIEEIDELIEKHLRNWSL--DRLAIVERA 79

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 219114260 155 ALRIGATQLLFLK-VPEHAAVKETVELLRhdpKTTVPESrIKFVNAVLRRISRE 207
Cdd:cd00619   80 ILRLAVYELLFLPdVPHPVVINEAIELAK---RFGGDDS-HKFVNGVLDKIAKD 129
nusB TIGR01951
transcription antitermination factor NusB; A transcription antitermination complex active in ...
 75-207 1.54e-10

transcription antitermination factor NusB; A transcription antitermination complex active in many bacteria was designated N-utilization substance (Nus) in E. coli because of its interaction with phage lambda protein N. This model represents NusB. Other components are NusA and NusG. NusE is, in fact, ribosomal protein S10. [Transcription, Transcription factors]


Pssm-ID: 273891 [Multi-domain]  Cd Length: 129  Bit Score: 58.66  E-value: 1.54e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260   75 RNARFLAARAL----ITKTGSAAFAVDRLESNKhystLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKETK-SRPNRVD 149
Cdd:TIGR01951   2 RKARELALQALyqweLSGEDVDEIIEEFLEERE----LDEEDREYFRELVRGVLENQEEIDELISPHLEDWTlERLDPVD 77

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 219114260  150 QfvqAALRIGATQLLFLK-VPEHAAVKETVELLRhdpKTTVPESRiKFVNAVLRRISRE 207
Cdd:TIGR01951  78 R---AILRLAIYELLYRPdVPYKVVINEAVELAK---KFGDEDSH-KFVNGVLDKIAKE 129
nusB PRK00202
transcription antitermination factor NusB;
75-207 1.89e-09

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 55.57  E-value: 1.89e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260  75 RNARFLAARAL----ITKTgsaaFAVDRLESNKHYSTLSTRDRSFARLLVTTTERRLGQIDEVLRQCQKETKsrPNRVDQ 150
Cdd:PRK00202   4 RKAREAAVQALyqweLSGN----DIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLKDWT--LERLDP 77

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 219114260 151 FVQAALRIGATQLLFLK-VPEHAAVKETVELlrhdPKTTVPESRIKFVNAVLRRISRE 207
Cdd:PRK00202  78 VERAILRLALYELLFRDdVPYKVVINEAIEL----AKKFGDEDSHKFVNGVLDKIAKE 131
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 329-395 3.30e-08

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: 53.58  E-value: 3.30e-08
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 219114260  329 KNGETsvagldVVDMCASPGGKT---AQLwNYGFASVTAVEVAEKRTERLRQNMQRLNMDCEVVV-ADGAQ 395
Cdd:pfam01189   7 QEGET------ILDMCAAPGGKTthiAEL-MKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILnGDGRQ 70
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 340-396 2.93e-04

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 39.85  E-value: 2.93e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 219114260  340 VVDMCASPGGKTAQLWNYGFASVTAVEVAEKRTERLRQNMQRLNMDCEVVVADGAQW 396
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGGARVTGVDLSPEMLERARERAAEAGLNVEFVQGDAEDL 57
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 339-396 7.97e-04

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: 38.57  E-value: 7.97e-04
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*....
gi 219114260 339 DVVDMCASPGGKTAQLWNYGFASVTAVEVAEKRTERLRQNMQRLNMD-CEVVVADGAQW 396
Cdd:cd02440    1 RVLDLGCGTGALALALASGPGARVTGVDISPVALELARKAAAALLADnVEVLKGDAEEL 59
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
317-396 9.62e-03

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 37.19  E-value: 9.62e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 219114260 317 TTPAIA---LYNALSKNGetsVAGLDVVDMCASPG--GKTAQLwnYGFASVTAVEVAEKRTERLRQNMQRLNMDCEVVVA 391
Cdd:COG2263   26 TPAELAaelLHLAYLRGD---IEGKTVLDLGCGTGmlAIGAAL--LGAKKVVGVDIDPEALEIARENAERLGVRVDFIRA 100


                 ....*
gi 219114260 392 DGAQW 396
Cdd:COG2263  101 DVTRI 105
 
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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