|
Name |
Accession |
Description |
Interval |
E-value |
| PRK14902 |
PRK14902 |
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB; |
1-434 |
0e+00 |
|
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
Pssm-ID: 237857 [Multi-domain] Cd Length: 444 Bit Score: 688.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 1 MMKSVRTYALETINDVLNKGAYSNLKINEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKT--KIKSWVRQLL 78
Cdd:PRK14902 1 MKMNARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIKKrkKLDPWVRNLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 79 WMSLYQYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRTELPSFEDIDDTKKRIAIQYSLPKWIVDHWVTH 158
Cdd:PRK14902 81 RMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNILREGLPDIDEIKDPVKRLSIKYSHPVWLVKRWIDQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 159 FGIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLHISGLPVVNSNAFKEGYISIQDKSSM 238
Cdd:PRK14902 161 YGEEKAEKILESLNEPPKASIRVNTLKISVEELIEKLEEEGYEVEESLLSPEALVIEKGNIAGTDLFKDGLITIQDESSM 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 239 MVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEV---YNKM 315
Cdd:PRK14902 241 LVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVhekFAEK 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 316 YDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKD 395
Cdd:PRK14902 321 FDKILVDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEEVIEAFLEEHPE 400
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 488388003 396 FEFEPFQNPATGEQVK-----TLQILPQDFNSDGFFISKIKRKE 434
Cdd:PRK14902 401 FELVPLQHEKPDELVYevkdgYLQILPNDYGTDGFFIAKLRKKG 444
|
|
| RsmB |
COG0144 |
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ... |
43-434 |
9.46e-134 |
|
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: 391.68 E-value: 9.46e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 43 LFTELVYGTLKRKYTLDYLLKPFIKTKIKSWVRQLLWMSLYQYLYLDKIPNHAIIHEAVDIAKKRG------GYHTGNIV 116
Cdd:COG0144 38 LLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLLLLLLPLLAALLLVAAAQLLAARVavdeavGPGAAGLV 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 117 NGILRTVMRtELPSFEDIDDTKKRIAIQYSLPKWIVDHWVTHFGIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLE 196
Cdd:COG0144 118 NAVLRRVLR-EREALLAAADPVERLAVRYSHPEWLVERLRAAYGPEEAEALLAALNEPPPLDLRVNTLKASREELLARLA 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 197 QEGYHVKKDDMLPFCLHI-SGLPVVNSNAFKEGYISIQDKSSMMVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGH 275
Cdd:COG0144 197 EEGIEAEPTPLSPDGLRLeGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGR 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 276 VDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEV---YNKMYDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVEL 352
Cdd:COG0144 277 VVAVDISEHRLKRLRENLARLGLSNVEVVVADARELlewLPGKFDRVLLDAPCSGTGTLRRHPDIKWRRTPEDIAELAAL 356
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 353 QLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKDFEFEPFQNPATGEQV---KTLQILPQDFNSDGFFISK 429
Cdd:COG0144 357 QRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALtdgGYLRLLPHRHGTDGFFIAR 436
|
....*
gi 488388003 430 IKRKE 434
Cdd:COG0144 437 LRKKA 441
|
|
| rsmB |
TIGR00563 |
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ... |
6-433 |
1.05e-112 |
|
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: 337.61 E-value: 1.05e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 6 RTYALETINDVLNKGAYSNLKINevlSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIK--TKIKSWVRQLLWMSLY 83
Cdd:TIGR00563 1 RSIAAQALEQLEQGQSLSNLLPP---LQQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDrpMKGKPRTVHYLILVGL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 84 QYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRTElpsfEDIDDTKKRIAIQYSLPKWIVDH-WVTHFGie 162
Cdd:TIGR00563 78 YQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQREQ----EELLAEFNALDARYLHPEWLVKRlQKAYPG-- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 163 KTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLHI-SGLPVVNSNAFKEGYISIQDKSSMMVA 241
Cdd:TIGR00563 152 QWQSICEANNQRPPMWLRINRTKHSRDEWLALLAEAGMKGFPHDLAPDAVRLeTPAAVHALPGFEEGWVTVQDASAQWVA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 242 YVMNLGRDDKVLDACSAPGGKACHMAEiLSPEGHVDATDIHEHKINLIKQNIKKLKLNnIKAFQHDATEVY------NKM 315
Cdd:TIGR00563 232 TWLAPQNEETILDACAAPGGKTTHILE-LAPQAQVVALDIHEHRLKRVYENLKRLGLT-IKAETKDGDGRGpsqwaeNEQ 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 316 YDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKD 395
Cdd:TIGR00563 310 FDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPEENSEQIKAFLQEHPD 389
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 488388003 396 FEFEPFQNPatgEQVKT--LQILPQDFNSDGFFISKIKRK 433
Cdd:TIGR00563 390 FPFEKTGTP---EQVRDggLQILPHAEEGDGFFYAKLIKK 426
|
|
| Methyltr_RsmB-F |
pfam01189 |
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ... |
241-431 |
2.09e-60 |
|
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: 195.34 E-value: 2.09e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 241 AYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATE----VYNKMY 316
Cdd:pfam01189 1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQpdqwLGGVLF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 317 DKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKDF 396
Cdd:pfam01189 81 DRILLDAPCSGTGVIRRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAVIEYFLQKHPDV 160
|
170 180 190
....*....|....*....|....*....|....*....
gi 488388003 397 EFEPFQ-NPATGEQVK---TLQILPQDFNSDGFFISKIK 431
Cdd:pfam01189 161 ELVPTPlFEPVGLAIGeqpTLRLLPHTHNGDGFFIAKLR 199
|
|
| Methyltransferase_Sun |
cd00620 |
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ... |
3-127 |
4.35e-32 |
|
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: 118.21 E-value: 4.35e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 3 KSVRTYALETINDVLNKGAYSNLKINEVLSTNNiNTVDKNLFTELVYGTLKRKYTLDYLLKPFIK---TKIKSWVRQLLW 79
Cdd:cd00620 1 MNARSTAAEVLRDVLQRGASLNAVLSALQKKDK-SDRDRGLATELVYGTLRWLALLDWIINPLLKkpdVGKDPDVRNLLR 79
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 488388003 80 MSLYQYLYLDkIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRTE 127
Cdd:cd00620 80 LGLYQLLYLD-VPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERED 126
|
|
| |
|
Name |
Accession |
Description |
Interval |
E-value |
| PRK14902 |
PRK14902 |
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB; |
1-434 |
0e+00 |
|
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
Pssm-ID: 237857 [Multi-domain] Cd Length: 444 Bit Score: 688.84 E-value: 0e+00
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 1 MMKSVRTYALETINDVLNKGAYSNLKINEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKT--KIKSWVRQLL 78
Cdd:PRK14902 1 MKMNARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYLAPFIKKrkKLDPWVRNLL 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 79 WMSLYQYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRTELPSFEDIDDTKKRIAIQYSLPKWIVDHWVTH 158
Cdd:PRK14902 81 RMSLYQLLYLDKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNILREGLPDIDEIKDPVKRLSIKYSHPVWLVKRWIDQ 160
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 159 FGIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLHISGLPVVNSNAFKEGYISIQDKSSM 238
Cdd:PRK14902 161 YGEEKAEKILESLNEPPKASIRVNTLKISVEELIEKLEEEGYEVEESLLSPEALVIEKGNIAGTDLFKDGLITIQDESSM 240
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 239 MVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEV---YNKM 315
Cdd:PRK14902 241 LVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDARKVhekFAEK 320
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 316 YDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKD 395
Cdd:PRK14902 321 FDKILVDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEEVIEAFLEEHPE 400
|
410 420 430 440
....*....|....*....|....*....|....*....|....
gi 488388003 396 FEFEPFQNPATGEQVK-----TLQILPQDFNSDGFFISKIKRKE 434
Cdd:PRK14902 401 FELVPLQHEKPDELVYevkdgYLQILPNDYGTDGFFIAKLRKKG 444
|
|
| RsmB |
COG0144 |
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ... |
43-434 |
9.46e-134 |
|
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: 391.68 E-value: 9.46e-134
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 43 LFTELVYGTLKRKYTLDYLLKPFIKTKIKSWVRQLLWMSLYQYLYLDKIPNHAIIHEAVDIAKKRG------GYHTGNIV 116
Cdd:COG0144 38 LLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLLLLLLPLLAALLLVAAAQLLAARVavdeavGPGAAGLV 117
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 117 NGILRTVMRtELPSFEDIDDTKKRIAIQYSLPKWIVDHWVTHFGIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLE 196
Cdd:COG0144 118 NAVLRRVLR-EREALLAAADPVERLAVRYSHPEWLVERLRAAYGPEEAEALLAALNEPPPLDLRVNTLKASREELLARLA 196
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 197 QEGYHVKKDDMLPFCLHI-SGLPVVNSNAFKEGYISIQDKSSMMVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGH 275
Cdd:COG0144 197 EEGIEAEPTPLSPDGLRLeGPGPVTALPGFREGLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGR 276
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 276 VDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEV---YNKMYDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVEL 352
Cdd:COG0144 277 VVAVDISEHRLKRLRENLARLGLSNVEVVVADARELlewLPGKFDRVLLDAPCSGTGTLRRHPDIKWRRTPEDIAELAAL 356
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 353 QLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKDFEFEPFQNPATGEQV---KTLQILPQDFNSDGFFISK 429
Cdd:COG0144 357 QRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALtdgGYLRLLPHRHGTDGFFIAR 436
|
....*
gi 488388003 430 IKRKE 434
Cdd:COG0144 437 LRKKA 441
|
|
| PRK14901 |
PRK14901 |
16S rRNA methyltransferase B; Provisional |
6-433 |
3.25e-114 |
|
16S rRNA methyltransferase B; Provisional
Pssm-ID: 237856 [Multi-domain] Cd Length: 434 Bit Score: 341.52 E-value: 3.25e-114
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 6 RTYALETINDVlNKGAYSNLKINEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKTKIKSW---VRQLLWMSL 82
Cdd:PRK14901 4 RQLAWEILQAV-ARGAYADVALERVLRKYPLSGADRALVTELVYGCIRRRRTLDAWIDQLGKKPAHKQppdLRWLLHLGL 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 83 YQYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRT-------ELPSfedidDTKKRIAIQYSLPKWIVDHW 155
Cdd:PRK14901 83 YQLRYMDRIPASAAVNTTVELAKQNGLGGLAGVVNGILRQYLRAreagdplPLPE-----DPIERLAILHSFPDWLVKLW 157
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 156 VTHFGIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLHISG-------LPvvnsnAFKEG 228
Cdd:PRK14901 158 LEWLGLEEAEQLCKWFNQPPSLDLRINPLRTSLEEVQAALAEAGITATPIPGLPQGLRLTGnpgsirqLP-----GYEEG 232
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 229 YISIQDKSSMMVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDA 308
Cdd:PRK14901 233 WWTVQDRSAQLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADS 312
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 309 TEV------YNKMYDKILVDAPCSGLGVL-RHkPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQME 381
Cdd:PRK14901 313 RNLlelkpqWRGYFDRILLDAPCSGLGTLhRH-PDARWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYATCTLHPAE 391
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|..
gi 488388003 382 NENVIYTFLKKHKDFEFEPFQnpatgeqvktLQILPQDFNSDGFFISKIKRK 433
Cdd:PRK14901 392 NEAQIEQFLARHPDWKLEPPK----------QKIWPHRQDGDGFFMAVLRKK 433
|
|
| rsmB |
TIGR00563 |
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ... |
6-433 |
1.05e-112 |
|
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: 337.61 E-value: 1.05e-112
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 6 RTYALETINDVLNKGAYSNLKINevlSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIK--TKIKSWVRQLLWMSLY 83
Cdd:TIGR00563 1 RSIAAQALEQLEQGQSLSNLLPP---LQQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDrpMKGKPRTVHYLILVGL 77
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 84 QYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRTElpsfEDIDDTKKRIAIQYSLPKWIVDH-WVTHFGie 162
Cdd:TIGR00563 78 YQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQREQ----EELLAEFNALDARYLHPEWLVKRlQKAYPG-- 151
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 163 KTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLHI-SGLPVVNSNAFKEGYISIQDKSSMMVA 241
Cdd:TIGR00563 152 QWQSICEANNQRPPMWLRINRTKHSRDEWLALLAEAGMKGFPHDLAPDAVRLeTPAAVHALPGFEEGWVTVQDASAQWVA 231
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 242 YVMNLGRDDKVLDACSAPGGKACHMAEiLSPEGHVDATDIHEHKINLIKQNIKKLKLNnIKAFQHDATEVY------NKM 315
Cdd:TIGR00563 232 TWLAPQNEETILDACAAPGGKTTHILE-LAPQAQVVALDIHEHRLKRVYENLKRLGLT-IKAETKDGDGRGpsqwaeNEQ 309
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 316 YDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKD 395
Cdd:TIGR00563 310 FDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPEENSEQIKAFLQEHPD 389
|
410 420 430 440
....*....|....*....|....*....|....*....|
gi 488388003 396 FEFEPFQNPatgEQVKT--LQILPQDFNSDGFFISKIKRK 433
Cdd:TIGR00563 390 FPFEKTGTP---EQVRDggLQILPHAEEGDGFFYAKLIKK 426
|
|
| PRK14904 |
PRK14904 |
16S rRNA methyltransferase B; Provisional |
1-400 |
1.24e-80 |
|
16S rRNA methyltransferase B; Provisional
Pssm-ID: 237858 [Multi-domain] Cd Length: 445 Bit Score: 255.75 E-value: 1.24e-80
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 1 MMKSvRTYALETINDVLNKGAYSNLKINEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKTKIKS---WVRQL 77
Cdd:PRK14904 1 MMTA-RELALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFYHHDLEKaapVLKNI 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 78 LWMSLYQYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMrtelPSFEDIDD-TK-----KRIAIQYSLPKWI 151
Cdd:PRK14904 80 LRLGVYQLLFLDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLRNIS----PETISLDEwLKgmpeaERLSLLYSHPEWL 155
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 152 VDHWVTHFGIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEgyHVKKDDmlpfclhiSGLP-VVNSNAF----- 225
Cdd:PRK14904 156 LERWIARYGEERTEAMLSYNNQAPLFGFRINRLKTTPEKFLAAPADA--SVTFEK--------SGLPnFFLSKDFslfep 225
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 226 --KEGYISIQDKSSMMVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKA 303
Cdd:PRK14904 226 flKLGLVSVQNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIET 305
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 304 FQHDATEV-YNKMYDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMEN 382
Cdd:PRK14904 306 IEGDARSFsPEEQPDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATCSIEPEEN 385
|
410
....*....|....*...
gi 488388003 383 ENVIYTFLKKHKDFEFEP 400
Cdd:PRK14904 386 ELQIEAFLQRHPEFSAEP 403
|
|
| PRK10901 |
PRK10901 |
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB; |
2-432 |
7.89e-77 |
|
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
Pssm-ID: 236790 [Multi-domain] Cd Length: 427 Bit Score: 245.10 E-value: 7.89e-77
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 2 MKSVRTYALETINDVLNKGAysNLKinEVLST--NNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKTKIK---SWVRQ 76
Cdd:PRK10901 1 SMNLRALAAAAILQVVDQGQ--SLS--AALPAlqQKVSDKDRALLQELCYGVLRRLPRLEWLIAQLLAKPLKgkqRIVHA 76
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 77 LLWMSLYQYLYLdKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMR--TELPSFEDIDDTkkriaIQYSLPKWIV-- 152
Cdd:PRK10901 77 LLLVGLYQLLYT-RIPAHAAVDETVEAAKALKRPWAKGLVNAVLRRFQReqEELLAELQADPV-----ARYNHPSWLIkr 150
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 153 ------DHWvthfgiektENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLH------ISGLPvv 220
Cdd:PRK10901 151 lkkaypEQW---------QAILAANNQRPPMWLRVNRRHHSRDAYLALLAEAGIEAFPHAVGPDAIRletpvpVHQLP-- 219
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 221 nsnAFKEGYISIQDKSSMMVAYVMNLGRDDKVLDACSAPGGKACHMAEiLSPEGHVDATDIHEHKINLIKQNIKKLKLN- 299
Cdd:PRK10901 220 ---GFAEGWVSVQDAAAQLAATLLAPQNGERVLDACAAPGGKTAHILE-LAPQAQVVALDIDAQRLERVRENLQRLGLKa 295
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 300 NIKAFQHDATEVY--NKMYDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTI 377
Cdd:PRK10901 296 TVIVGDARDPAQWwdGQPFDRILLDAPCSATGVIRRHPDIKWLRRPEDIAALAALQSEILDALWPLLKPGGTLLYATCSI 375
|
410 420 430 440 450
....*....|....*....|....*....|....*....|....*....|....*.
gi 488388003 378 EQMENENVIYTFLKKHKDFEFEPFQNPATGEQvktlQILPQDFNSDGFFISK-IKR 432
Cdd:PRK10901 376 LPEENEQQIKAFLARHPDAELLDTGTPQQPGR----QLLPGEEDGDGFFYALlIKR 427
|
|
| PRK14903 |
PRK14903 |
16S rRNA methyltransferase B; Provisional |
1-398 |
5.81e-70 |
|
16S rRNA methyltransferase B; Provisional
Pssm-ID: 184896 [Multi-domain] Cd Length: 431 Bit Score: 227.83 E-value: 5.81e-70
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 1 MMKSVRTYALETINDVLNKGAYSNLKINEVLSTnnINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKTK-IKSWVRQLLW 79
Cdd:PRK14903 1 MKTNVRLLAYRLLRKYEKEKFIFREDVDSVLSF--LDDKDRRFFKELVWGVVRKEELLDWYINQLLKKKdIPPAVRVALR 78
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 80 MSLYQYLYLDKIPNHAIIHEAVDIAKKRggyHTGNIVNGILRTVMRTELPsfediddtkKRIAIQYSLPKWIVDHWVTHF 159
Cdd:PRK14903 79 MGAYQLLFMNSVPDYAAVSETVKLVKNE---NFKKLVNAVLRRLRTVPEP---------KELHLKYSHPKWLVNYWRSFL 146
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 160 GIEKTENIAQSFLEPIATTVRANISRGSIDSIISKLEQEGYHVKKDDMLPFCLHIS--GLPVVNSNAFKEGYISIQDKSS 237
Cdd:PRK14903 147 PEEAVLRIMEWNQEPLPTMLRVNSLAITREEVIKILAEEGTEAVPGKHSPFSLIVRklGVNMNDSRVIKDGLATVQGESS 226
|
250 260 270 280 290 300 310 320
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 238 MMVAYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDA---TEVYNK 314
Cdd:PRK14903 227 QIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADAerlTEYVQD 306
|
330 340 350 360 370 380 390 400
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 315 MYDKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHK 394
Cdd:PRK14903 307 TFDRILVDAPCTSLGTARNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKRFVYEQK 386
|
....
gi 488388003 395 DFEF 398
Cdd:PRK14903 387 DAEV 390
|
|
| Methyltr_RsmB-F |
pfam01189 |
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ... |
241-431 |
2.09e-60 |
|
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: 195.34 E-value: 2.09e-60
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 241 AYVMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATE----VYNKMY 316
Cdd:pfam01189 1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQpdqwLGGVLF 80
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 317 DKILVDAPCSGLGVLRHKPEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKDF 396
Cdd:pfam01189 81 DRILLDAPCSGTGVIRRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAVIEYFLQKHPDV 160
|
170 180 190
....*....|....*....|....*....|....*....
gi 488388003 397 EFEPFQ-NPATGEQVK---TLQILPQDFNSDGFFISKIK 431
Cdd:pfam01189 161 ELVPTPlFEPVGLAIGeqpTLRLLPHTHNGDGFFIAKLR 199
|
|
| nop2p |
TIGR00446 |
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ... |
179-432 |
1.39e-46 |
|
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base modification]
Pssm-ID: 188051 [Multi-domain] Cd Length: 264 Bit Score: 161.48 E-value: 1.39e-46
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 179 VRANISRGSIDSIISKLEQEGYHVKKDDmLPFCLHI--SGLPVVNSNAFKEGYISIQDKSSMMVAYVMNLGRDDKVLDAC 256
Cdd:TIGR00446 1 IRVNTLKINVEDLLERLENRGVVLEPTC-EEYFFEVkeSPFSIGSTPEYLFGYYYPQEASSMIPPIALEPREDERVLDMA 79
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 257 SAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEV--YNKMYDKILVDAPCSGLGVLRHK 334
Cdd:TIGR00446 80 AAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVINADGRKFgaYLLKFDAILLDAPCSGEGVIRKD 159
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 335 PEIKYSQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKDFEFEPFQ-------NPATG 407
Cdd:TIGR00446 160 PSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVEEIIKgdeffgiNIGKG 239
|
250 260
....*....|....*....|....*
gi 488388003 408 EQVKTLQILPQDFNSDGFFISKIKR 432
Cdd:TIGR00446 240 EVKGALRVFPQNYDCEGFFVAKLRK 264
|
|
| NusB |
pfam01029 |
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ... |
4-125 |
6.82e-34 |
|
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: 123.53 E-value: 6.82e-34
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 4 SVRTYALETINDV-------LNKGAYSNLKINEVLsTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIK----TKIKS 72
Cdd:pfam01029 2 NARELALQALYQVeingsdeEEKGAYLNEALDKAL-EGDLSEEDRAFATELVYGVLRNLEELDALIEKLLEnwplERLSP 80
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|...
gi 488388003 73 WVRQLLWMSLYQYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMR 125
Cdd:pfam01029 81 VDRAILRLGLYELLFLDDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVAR 133
|
|
| Methyltransferase_Sun |
cd00620 |
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ... |
3-127 |
4.35e-32 |
|
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: 118.21 E-value: 4.35e-32
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 3 KSVRTYALETINDVLNKGAYSNLKINEVLSTNNiNTVDKNLFTELVYGTLKRKYTLDYLLKPFIK---TKIKSWVRQLLW 79
Cdd:cd00620 1 MNARSTAAEVLRDVLQRGASLNAVLSALQKKDK-SDRDRGLATELVYGTLRWLALLDWIINPLLKkpdVGKDPDVRNLLR 79
|
90 100 110 120
....*....|....*....|....*....|....*....|....*...
gi 488388003 80 MSLYQYLYLDkIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRTE 127
Cdd:cd00620 80 LGLYQLLYLD-VPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRFERED 126
|
|
| NusB |
COG0781 |
Transcription antitermination protein NusB [Transcription]; |
8-126 |
7.73e-31 |
|
Transcription antitermination protein NusB [Transcription];
Pssm-ID: 440544 [Multi-domain] Cd Length: 128 Bit Score: 114.86 E-value: 7.73e-31
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 8 YALETINDVLNKGAYSNLKINEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKT----KIKSWVRQLLWMSLY 83
Cdd:COG0781 2 LALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIAPYLKDwpleRLDPVDRAILRLAAY 81
|
90 100 110 120
....*....|....*....|....*....|....*....|...
gi 488388003 84 QYLYLDKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMRT 126
Cdd:COG0781 82 ELLYLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKE 124
|
|
| yebU |
PRK11933 |
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed |
197-435 |
7.13e-30 |
|
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
Pssm-ID: 183387 [Multi-domain] Cd Length: 470 Bit Score: 120.78 E-value: 7.13e-30
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 197 QEGYHVKKDDMLPFCL-----HISGLpvvnsnaFkegYIsiQDKSSMM--VAYVMNLGRDDKVLDACSAPGGKACHMAEI 269
Cdd:PRK11933 67 EEGFWIERDDEDALPLgntaeHLSGL-------F---YI--QEASSMLpvAALFADDNAPQRVLDMAAAPGSKTTQIAAL 134
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 270 LSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDAtEVYNK----MYDKILVDAPCSGLGVLRHKPEIKYSQSQNS 345
Cdd:PRK11933 135 MNNQGAIVANEYSASRVKVLHANISRCGVSNVALTHFDG-RVFGAalpeTFDAILLDAPCSGEGTVRKDPDALKNWSPES 213
|
170 180 190 200 210 220 230 240
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 346 IKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENVIYTFLKKHKD-FEFEPFQNPATG-EQVKT----LQILPQD 419
Cdd:PRK11933 214 NLEIAATQRELIESAFHALKPGGTLVYSTCTLNREENQAVCLWLKETYPDaVEFEPLGDLFPGaEKALTeegfLHVFPQI 293
|
250
....*....|....*.
gi 488388003 420 FNSDGFFISKIKRKES 435
Cdd:PRK11933 294 YDSEGFFVARLRKTAS 309
|
|
| NusB_Sun |
cd00447 |
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ... |
4-125 |
1.03e-21 |
|
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: 90.10 E-value: 1.03e-21
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 4 SVRTYALETINDVLNKGAYSNLKINEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIK-------TKIKSWVRQ 76
Cdd:cd00447 1 SAREIAFQALYQVEIRNGISLEAVLSALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKkwlldrlDKVDRAILR 80
|
90 100 110 120
....*....|....*....|....*....|....*....|....*....
gi 488388003 77 LLWMSLYQYLYldKIPNHAIIHEAVDIAKKRGGYHTGNIVNGILRTVMR 125
Cdd:cd00447 81 LLLYELYQLLY--DVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIAK 127
|
|
| nusB |
TIGR01951 |
transcription antitermination factor NusB; A transcription antitermination complex active in ... |
27-125 |
8.34e-13 |
|
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: 65.21 E-value: 8.34e-13
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 27 INEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKTkiksW--------VRQLLWMSLYQYLYLDKIPNHAIIH 98
Cdd:TIGR01951 26 IEEFLEERELDEEDREYFRELVRGVLENQEEIDELISPHLED----WtlerldpvDRAILRLAIYELLYRPDVPYKVVIN 101
|
90 100
....*....|....*....|....*..
gi 488388003 99 EAVDIAKKRGGYHTGNIVNGILRTVMR 125
Cdd:TIGR01951 102 EAVELAKKFGDEDSHKFVNGVLDKIAK 128
|
|
| nusB |
PRK00202 |
transcription antitermination factor NusB; |
27-120 |
2.52e-11 |
|
transcription antitermination factor NusB;
Pssm-ID: 234686 [Multi-domain] Cd Length: 137 Bit Score: 60.96 E-value: 2.52e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 27 INEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKtkikSW--------VRQLLWMSLYQYLYLDKIPNHAIIH 98
Cdd:PRK00202 28 IEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISPYLK----DWtlerldpvERAILRLALYELLFRDDVPYKVVIN 103
|
90 100
....*....|....*....|..
gi 488388003 99 EAVDIAKKRGGYHTGNIVNGIL 120
Cdd:PRK00202 104 EAIELAKKFGDEDSHKFVNGVL 125
|
|
| Terminator_NusB |
cd00619 |
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ... |
27-125 |
7.74e-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: 59.60 E-value: 7.74e-11
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 27 INEVLSTNNINTVDKNLFTELVYGTLKRKYTLDYLLKPFIKTKIKSWVRQL----LWMSLYQYLYLDKIPNHAIIHEAVD 102
Cdd:cd00619 26 VSLLELLQYKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLDRLAIVeraiLRLAVYELLFLPDVPHPVVINEAIE 105
|
90 100
....*....|....*....|...
gi 488388003 103 IAKKRGGYHTGNIVNGILRTVMR 125
Cdd:cd00619 106 LAKRFGGDDSHKFVNGVLDKIAK 128
|
|
| AdoMet_MTases |
cd02440 |
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ... |
251-373 |
9.81e-09 |
|
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: 52.82 E-value: 9.81e-09
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 251 KVLDACSAPGGKACHMAEilSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEVY---NKMYDKILVDAPCSg 327
Cdd:cd02440 1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPpeaDESFDVIISDPPLH- 77
|
90 100 110 120
....*....|....*....|....*....|....*....|....*.
gi 488388003 328 lgvlrhkpeikysqsqnsikSLVELQLQILENVKDNIKPGGTIVYS 373
Cdd:cd02440 78 --------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
|
|
| Gcd14 |
COG2519 |
tRNA A58 N-methylase Trm61 [Translation, ribosomal structure and biogenesis]; tRNA A58 ... |
236-381 |
9.35e-07 |
|
tRNA A58 N-methylase Trm61 [Translation, ribosomal structure and biogenesis]; tRNA A58 N-methylase Trm61 is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 442009 [Multi-domain] Cd Length: 249 Bit Score: 49.77 E-value: 9.35e-07
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 236 SSMMVAYvMNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKL-NNIKAFQHDATEVY-N 313
Cdd:COG2519 80 AGYIIAR-LDIFPGARVLEAGTGSGALTLALARAVGPEGKVYSYERREDFAEIARKNLERFGLpDNVELKLGDIREGIdE 158
|
90 100 110 120 130 140
....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 488388003 314 KMYDKILVDAPcsglgvlrhKPEikysqsqnsikslvelqlQILENVKDNIKPGGTIV-YSTcTIEQME 381
Cdd:COG2519 159 GDVDAVFLDMP---------DPW------------------EALEAVAKALKPGGVLVaYVP-TVNQVS 199
|
|
| Methyltransf_31 |
pfam13847 |
Methyltransferase domain; This family appears to have methyltransferase activity. |
246-387 |
1.11e-06 |
|
Methyltransferase domain; This family appears to have methyltransferase activity.
Pssm-ID: 463998 [Multi-domain] Cd Length: 150 Bit Score: 48.18 E-value: 1.11e-06
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 246 LGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATE----VYNKMYDKILV 321
Cdd:pfam13847 1 IDKGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDIEElpelLEDDKFDVVIS 80
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 488388003 322 dapcsglgvlrhkpeikysqsqNSIKSLVELQLQILENVKDNIKPGGTIVYSTC-----TIEQMENENVIY 387
Cdd:pfam13847 81 ----------------------NCVLNHIPDPDKVLQEILRVLKPGGRLIISDPdslaeLPAHVKEDSTYY 129
|
|
| SmtA |
COG0500 |
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ... |
246-373 |
3.37e-05 |
|
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];
Pssm-ID: 440266 [Multi-domain] Cd Length: 199 Bit Score: 44.52 E-value: 3.37e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 246 LGRDDKVLDACSAPGGKACHMAEILSpeGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATE---VYNKMYDKILVd 322
Cdd:COG0500 24 LPKGGRVLDLGCGTGRNLLALAARFG--GRVIGIDLSPEAIALARARAAKAGLGNVEFLVADLAEldpLPAESFDLVVA- 100
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|.
gi 488388003 323 apcsgLGVLRHKPEikysqsqnsikslvELQLQILENVKDNIKPGGTIVYS 373
Cdd:COG0500 101 -----FGVLHHLPP--------------EEREALLRELARALKPGGVLLLS 132
|
|
| TrmR |
COG4122 |
tRNA 5-hydroxyU34 O-methylase TrmR/YrrM [Translation, ribosomal structure and biogenesis]; ... |
265-371 |
3.70e-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: 44.02 E-value: 3.70e-05
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 265 HMAEILSPEGHVDATDIHEHKINLIKQNIKKLKL-NNIKAFQHDATEVYNKM----YDKILVDAPcsglgvlrhkpeiky 339
Cdd:COG4122 33 WLARALPDDGRLTTIEIDPERAAIARENFARAGLaDRIRLILGDALEVLPRLadgpFDLVFIDAD--------------- 97
|
90 100 110
....*....|....*....|....*....|..
gi 488388003 340 sqsqnsiKSLVelqLQILENVKDNIKPGGTIV 371
Cdd:COG4122 98 -------KSNY---PDYLELALPLLRPGGLIV 119
|
|
| CobL |
COG2242 |
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part ... |
244-393 |
2.30e-04 |
|
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis
Pssm-ID: 441843 [Multi-domain] Cd Length: 403 Bit Score: 43.23 E-value: 2.30e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 244 MNLGRDDKVLD--ACSapGGKACHMAeILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEVYNKM--YDKI 319
Cdd:COG2242 243 LALRPGDVLWDigAGS--GSVSIEAA-RLAPGGRVYAIERDPERAALIRANARRFGVPNVEVVEGEAPEALADLpdPDAV 319
|
90 100 110 120 130 140 150
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 488388003 320 LVdapcsGlGvlrhkpeikysqsqnSIKSLVElqlqILENVKDNIKPGGTIVYSTCTIeqmENENVIYTFLKKH 393
Cdd:COG2242 320 FI-----G-G---------------SGGNLPE----ILEACWARLRPGGRLVANAVTL---ETLALALEALAEL 365
|
|
| Trm11 |
COG1041 |
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ... |
237-393 |
4.64e-04 |
|
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification
Pssm-ID: 440663 [Multi-domain] Cd Length: 172 Bit Score: 40.70 E-value: 4.64e-04
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 237 SMMVAY---VMNLGR---DDKVLDACSAPGG---KACHMAeilspeGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHD 307
Cdd:COG1041 9 SLDPRLaraLVNLAGakeGDTVLDPFCGTGTiliEAGLLG------RRVIGSDIDPKMVEGARENLEHYGYEDADVIRGD 82
|
90 100 110 120 130 140 150 160
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 308 ATEVYNKM--YDKILVDAPcsgLGVlrhkpeikysQSQNSIKSLVELQLQILENVKDNIKPGGTIVYSTCTIEQMENENV 385
Cdd:COG1041 83 ARDLPLADesVDAIVTDPP---YGR----------SSKISGEELLELYEKALEEAARVLKPGGRVVIVTPRDIDELLEEA 149
|
....*...
gi 488388003 386 IYTFLKKH 393
Cdd:COG1041 150 GFKVLERH 157
|
|
| UbiG |
COG2227 |
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ... |
246-374 |
1.27e-03 |
|
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis
Pssm-ID: 441829 [Multi-domain] Cd Length: 126 Bit Score: 38.85 E-value: 1.27e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 246 LGRDDKVLDACSAPGgkacHMAEILSPEGH-VDATDIHEHKINLIKQNIKKLklnNIKAFQHDATEV--YNKMYDKILVd 322
Cdd:COG2227 22 LPAGGRVLDVGCGTG----RLALALARRGAdVTGVDISPEALEIARERAAEL---NVDFVQGDLEDLplEDGSFDLVIC- 93
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|..
gi 488388003 323 apcsgLGVLRHKPEikysqsqnsikslvelQLQILENVKDNIKPGGTIVYST 374
Cdd:COG2227 94 -----SEVLEHLPD----------------PAALLRELARLLKPGGLLLLST 124
|
|
| cbiT |
PRK00377 |
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional |
246-382 |
1.46e-03 |
|
cobalt-precorrin-6Y C(15)-methyltransferase; Provisional
Pssm-ID: 234740 Cd Length: 198 Bit Score: 39.78 E-value: 1.46e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 246 LGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLK-LNNIKAFQHDATEVYNKMYDKilVDAP 324
Cdd:PRK00377 38 LRKGDMILDIGCGTGSVTVEASLLVGETGKVYAVDKDEKAINLTRRNAEKFGvLNNIVLIKGEAPEILFTINEK--FDRI 115
|
90 100 110 120 130
....*....|....*....|....*....|....*....|....*....|....*...
gi 488388003 325 CSGLGVLRhKPEIkysqsqnsIKSLVELqlqilenvkdnIKPGGTIVYSTCTIEQMEN 382
Cdd:PRK00377 116 FIGGGSEK-LKEI--------ISASWEI-----------IKKGGRIVIDAILLETVNN 153
|
|
| Methyltransf_25 |
pfam13649 |
Methyltransferase domain; This family appears to be a methyltransferase domain. |
252-368 |
2.34e-03 |
|
Methyltransferase domain; This family appears to be a methyltransferase domain.
Pssm-ID: 463945 [Multi-domain] Cd Length: 96 Bit Score: 37.16 E-value: 2.34e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 252 VLDACSAPGGKACHMAEILspEGHVDATDIHEHKINLIKQNIKKLKLnNIKAFQHDATE--VYNKMYDKILvdapCSGLG 329
Cdd:pfam13649 1 VLDLGCGTGRLTLALARRG--GARVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAEDlpFPDGSFDLVV----SSGVL 73
|
90 100 110
....*....|....*....|....*....|....*....
gi 488388003 330 VLRHKPEIKysqsqnsikslvelqlQILENVKDNIKPGG 368
Cdd:pfam13649 74 HHLPDPDLE----------------AALREIARVLKPGG 96
|
|
| PRK13942 |
PRK13942 |
protein-L-isoaspartate O-methyltransferase; Provisional |
239-323 |
3.09e-03 |
|
protein-L-isoaspartate O-methyltransferase; Provisional
Pssm-ID: 184409 Cd Length: 212 Bit Score: 38.84 E-value: 3.09e-03
10 20 30 40 50 60 70 80
....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 488388003 239 MVAYV---MNLGRDDKVLDACSAPGGKACHMAEILSPEGHVDATDIHEHKINLIKQNIKKLKLNNIKAFQHDATEVYNKM 315
Cdd:PRK13942 64 MVAIMcelLDLKEGMKVLEIGTGSGYHAAVVAEIVGKSGKVVTIERIPELAEKAKKTLKKLGYDNVEVIVGDGTLGYEEN 143
|
90
....*....|
gi 488388003 316 --YDKILVDA 323
Cdd:PRK13942 144 apYDRIYVTA 153
|
|
| |
