NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|896167232|ref|WP_049181007|]
View 

MULTISPECIES: RsmB/NOP family class I SAM-dependent RNA methyltransferase [Corynebacterium]

Protein Classification

RsmB/NOP family class I SAM-dependent RNA methyltransferase( domain architecture ID 11414805)

RsmB/NOP family class I SAM-dependent RNA methyltransferase similar to tRNA (cytosine(34)-C(5))-methyltransferase, which methylates cytosine at specific positions of intron-containing tRNA(Leu)(CAA) precursors and tRNA(Gly)(GCC) precursors

CATH:  2.20.25.110
EC:  2.1.1.-
Gene Ontology:  GO:0003723
PubMed:  12504684|12826405
SCOP:  3000118

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 47-485 1.69e-107

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: 326.58  E-value: 1.69e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  47 VALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLGTYQ 126
Cdd:COG0144    1 AAALAALRAEAAAAAAALALALLLLALLLLDRALAALLLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 127 LLRTRVDAYAAVDTSVR------AVAKVAGPGARGFVNAILRKVSSktESEWVAeiapdPATDPIGYVAMKHAHPRWIAM 200
Cdd:COG0144   81 LLLLPLLAALLLVAAAQllaarvAVDEAVGPGAAGLVNAVLRRVLR--EREALL-----AAADPVERLAVRYSHPEWLVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 201 EFARALGAQagELQQALAADDARPLVHLVARPGEITAEELALITG-----GEEGQWSPYCVRLD-SGAPGELEPVRQGLA 274
Cdd:COG0144  154 RLRAAYGPE--EAEALLAALNEPPPLDLRVNTLKASREELLARLAeegieAEPTPLSPDGLRLEgPGPVTALPGFREGLF 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 275 AVQDEGSQLIARAVtmAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGLP---VTVT 351
Cdd:COG0144  232 SVQDEASQLVALLL--DPKPGE---RVLDLCAAPGGKTLHLAELMGNKG-RVVAVDISEHRLKRLRENLARLGlsnVEVV 305

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 352 VADGRDTG--LETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRE 429
Cdd:COG0144  306 VADARELLewLPGKFDRVLLDAPCSGTGTLRRHPDIKWRRTPEDIAELAALQRELLDAAARLLKPGGRLVYSTCSLLPEE 385

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896167232 430 TRGIVDRAVTELPVTELSAHELVAPMTDVGPYPSVQMWPHRHGTDAMFFSVLRKND 485
Cdd:COG0144  386 NEEVVEAFLARHPDFELVPLAELLPGLALTDGGYLRLLPHRHGTDGFFIARLRKKA 441
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 47-485 1.69e-107

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: 326.58  E-value: 1.69e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  47 VALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLGTYQ 126
Cdd:COG0144    1 AAALAALRAEAAAAAAALALALLLLALLLLDRALAALLLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 127 LLRTRVDAYAAVDTSVR------AVAKVAGPGARGFVNAILRKVSSktESEWVAeiapdPATDPIGYVAMKHAHPRWIAM 200
Cdd:COG0144   81 LLLLPLLAALLLVAAAQllaarvAVDEAVGPGAAGLVNAVLRRVLR--EREALL-----AAADPVERLAVRYSHPEWLVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 201 EFARALGAQagELQQALAADDARPLVHLVARPGEITAEELALITG-----GEEGQWSPYCVRLD-SGAPGELEPVRQGLA 274
Cdd:COG0144  154 RLRAAYGPE--EAEALLAALNEPPPLDLRVNTLKASREELLARLAeegieAEPTPLSPDGLRLEgPGPVTALPGFREGLF 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 275 AVQDEGSQLIARAVtmAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGLP---VTVT 351
Cdd:COG0144  232 SVQDEASQLVALLL--DPKPGE---RVLDLCAAPGGKTLHLAELMGNKG-RVVAVDISEHRLKRLRENLARLGlsnVEVV 305

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 352 VADGRDTG--LETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRE 429
Cdd:COG0144  306 VADARELLewLPGKFDRVLLDAPCSGTGTLRRHPDIKWRRTPEDIAELAALQRELLDAAARLLKPGGRLVYSTCSLLPEE 385

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896167232 430 TRGIVDRAVTELPVTELSAHELVAPMTDVGPYPSVQMWPHRHGTDAMFFSVLRKND 485
Cdd:COG0144  386 NEEVVEAFLARHPDFELVPLAELLPGLALTDGGYLRLLPHRHGTDGFFIARLRKKA 441
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
44-483 8.91e-90

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 280.91  E-value: 8.91e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  44 PRKVALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIeASSSRPLSDIAGPVMDVLRLG 123
Cdd:PRK14902   5 ARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYL-APFIKKRKKLDPWVRNLLRMS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 124 TYQLLRT-RVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTESEwvaeiaPDPATDPIGYVAMKHAHPRWIAMEF 202
Cdd:PRK14902  84 LYQLLYLdKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNILREGLPD------IDEIKDPVKRLSIKYSHPVWLVKRW 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 203 ARALGAQAGElqQALAADDARPLVHLVARPGEITAEEL--ALITGG---EEGQWSPYCVRLDSGAPGELEPVRQGLAAVQ 277
Cdd:PRK14902 158 IDQYGEEKAE--KILESLNEPPKASIRVNTLKISVEELieKLEEEGyevEESLLSPEALVIEKGNIAGTDLFKDGLITIQ 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 278 DEGSQLIARAvtMAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGL---PVTVTVAD 354
Cdd:PRK14902 236 DESSMLVAPA--LDPKGGD---TVLDACAAPGGKTTHIAELLKNTG-KVVALDIHEHKLKLIEENAKRLgltNIETKALD 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 355 GR--DTGLETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRG 432
Cdd:PRK14902 310 ARkvHEKFAEKFDKILVDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEE 389

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 896167232 433 IVDRAVTELPVTELSahELVAPMTDVGPYPS----VQMWPHRHGTDAMFFSVLRK 483
Cdd:PRK14902 390 VIEAFLEEHPEFELV--PLQHEKPDELVYEVkdgyLQILPNDYGTDGFFIAKLRK 442
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 45-483 1.68e-65

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: 217.43  E-value: 1.68e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232   45 RKVALKVLADVREKDAYANLLLPKllkTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSdIAGPVMDVLRL-G 123
Cdd:TIGR00563   1 RSIAAQALEQLEQGQSLSNLLPPL---QQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDRPMK-GKPRTVHYLILvG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  124 TYQLLRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTEsewvaEIapdpaTDPIGYVAMKHAHPRWiameFA 203
Cdd:TIGR00563  77 LYQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQREQE-----EL-----LAEFNALDARYLHPEW----LV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  204 RALGAQAGELQQAL-AADDARPLVHLVARPGEITAEEL-----ALITGGEEGQWSPYCVRLDSGAP-GELEPVRQGLAAV 276
Cdd:TIGR00563 143 KRLQKAYPGQWQSIcEANNQRPPMWLRINRTKHSRDEWlallaEAGMKGFPHDLAPDAVRLETPAAvHALPGFEEGWVTV 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  277 QDEGSQLIARAvtMAPVAGEDSgrwLDLCSGPGGKSAFIGGIAAieGAKLDAVEVSATRAELVKKATT--GLPVTVTVAD 354
Cdd:TIGR00563 223 QDASAQWVATW--LAPQNEETI---LDACAAPGGKTTHILELAP--QAQVVALDIHEHRLKRVYENLKrlGLTIKAETKD 295

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  355 GRDTGL-----ETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRE 429
Cdd:TIGR00563 296 GDGRGPsqwaeNEQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPEE 375

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 896167232  430 TRGIVDRAVTELPVTELSAHELVAPMTDVGpypsVQMWPHRHGTDAMFFSVLRK 483
Cdd:TIGR00563 376 NSEQIKAFLQEHPDFPFEKTGTPEQVRDGG----LQILPHAEEGDGFFYAKLIK 425
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 287-482 5.27e-55

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: 182.62  E-value: 5.27e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  287 AVTMAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGLPVTVTV---ADGRDTGLETG 363
Cdd:pfam01189   1 AILLAPQEGE---TILDMCAAPGGKTTHIAELMKNQG-TVVAVDINKHRLKRVAENIHRLGVTNTIilnGDGRQPDQWLG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  364 ---FDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRGIVDRAVTE 440
Cdd:pfam01189  77 gvlFDRILLDAPCSGTGVIRRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAVIEYFLQK 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 896167232  441 LPVTELSAHELVAPM-TDVGPYPSVQMWPHRHGTDAMFFSVLR 482
Cdd:pfam01189 157 HPDVELVPTPLFEPVgLAIGEQPTLRLLPHTHNGDGFFIAKLR 199
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 45-164 4.68e-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: 118.98  E-value: 4.68e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  45 RKVALKVLADVREKDAYANLLLPKLLKtHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLGT 124
Cdd:cd00620    4 RSTAAEVLRDVLQRGASLNAVLSALQK-KDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGL 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 896167232 125 YQLLRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKV 164
Cdd:cd00620   83 YQLLYLDVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRF 122
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 47-485 1.69e-107

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: 326.58  E-value: 1.69e-107
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  47 VALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLGTYQ 126
Cdd:COG0144    1 AAALAALRAEAAAAAAALALALLLLALLLLDRALAALLLLAALRLLRRRDRALLAALLAGLLRLLRLLLLLLRLLLLLLL 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 127 LLRTRVDAYAAVDTSVR------AVAKVAGPGARGFVNAILRKVSSktESEWVAeiapdPATDPIGYVAMKHAHPRWIAM 200
Cdd:COG0144   81 LLLLPLLAALLLVAAAQllaarvAVDEAVGPGAAGLVNAVLRRVLR--EREALL-----AAADPVERLAVRYSHPEWLVE 153

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 201 EFARALGAQagELQQALAADDARPLVHLVARPGEITAEELALITG-----GEEGQWSPYCVRLD-SGAPGELEPVRQGLA 274
Cdd:COG0144  154 RLRAAYGPE--EAEALLAALNEPPPLDLRVNTLKASREELLARLAeegieAEPTPLSPDGLRLEgPGPVTALPGFREGLF 231

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 275 AVQDEGSQLIARAVtmAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGLP---VTVT 351
Cdd:COG0144  232 SVQDEASQLVALLL--DPKPGE---RVLDLCAAPGGKTLHLAELMGNKG-RVVAVDISEHRLKRLRENLARLGlsnVEVV 305

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 352 VADGRDTG--LETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRE 429
Cdd:COG0144  306 VADARELLewLPGKFDRVLLDAPCSGTGTLRRHPDIKWRRTPEDIAELAALQRELLDAAARLLKPGGRLVYSTCSLLPEE 385

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 896167232 430 TRGIVDRAVTELPVTELSAHELVAPMTDVGPYPSVQMWPHRHGTDAMFFSVLRKND 485
Cdd:COG0144  386 NEEVVEAFLARHPDFELVPLAELLPGLALTDGGYLRLLPHRHGTDGFFIARLRKKA 441
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
44-483 8.91e-90

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 280.91  E-value: 8.91e-90
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  44 PRKVALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIeASSSRPLSDIAGPVMDVLRLG 123
Cdd:PRK14902   5 ARELALEVLIKVENNGAYSNIALNKVLKKSELSDKDKALLTELVYGTIQRKLTLDYYL-APFIKKRKKLDPWVRNLLRMS 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 124 TYQLLRT-RVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTESEwvaeiaPDPATDPIGYVAMKHAHPRWIAMEF 202
Cdd:PRK14902  84 LYQLLYLdKVPDHAAVNEAVEIAKKRGHKGIAKFVNGVLRNILREGLPD------IDEIKDPVKRLSIKYSHPVWLVKRW 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 203 ARALGAQAGElqQALAADDARPLVHLVARPGEITAEEL--ALITGG---EEGQWSPYCVRLDSGAPGELEPVRQGLAAVQ 277
Cdd:PRK14902 158 IDQYGEEKAE--KILESLNEPPKASIRVNTLKISVEELieKLEEEGyevEESLLSPEALVIEKGNIAGTDLFKDGLITIQ 235

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 278 DEGSQLIARAvtMAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGL---PVTVTVAD 354
Cdd:PRK14902 236 DESSMLVAPA--LDPKGGD---TVLDACAAPGGKTTHIAELLKNTG-KVVALDIHEHKLKLIEENAKRLgltNIETKALD 309

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 355 GR--DTGLETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRG 432
Cdd:PRK14902 310 ARkvHEKFAEKFDKILVDAPCSGLGVIRRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYSTCTIEKEENEE 389

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 896167232 433 IVDRAVTELPVTELSahELVAPMTDVGPYPS----VQMWPHRHGTDAMFFSVLRK 483
Cdd:PRK14902 390 VIEAFLEEHPEFELV--PLQHEKPDELVYEVkdgyLQILPNDYGTDGFFIAKLRK 442
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 44-483 1.70e-67

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 222.88  E-value: 1.70e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  44 PRKVALKVLADVrEKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLG 123
Cdd:PRK14901   3 ARQLAWEILQAV-ARGAYADVALERVLRKYPLSGADRALVTELVYGCIRRRRTLDAWIDQLGKKPAHKQPPDLRWLLHLG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 124 TYQLLR-TRVDAYAAVDTSVRaVAKVAG-PGARGFVNAILRKVSSKTEsewvAEIAPDPATDPIGYVAMKHAHPRWIAME 201
Cdd:PRK14901  82 LYQLRYmDRIPASAAVNTTVE-LAKQNGlGGLAGVVNGILRQYLRARE----AGDPLPLPEDPIERLAILHSFPDWLVKL 156

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 202 FARALGAQagELQQALAADDARPLVHLVARPGEITAEEL--ALITGGEEGQWSPYC---VRLDS--GAPGELEPVRQGLA 274
Cdd:PRK14901 157 WLEWLGLE--EAEQLCKWFNQPPSLDLRINPLRTSLEEVqaALAEAGITATPIPGLpqgLRLTGnpGSIRQLPGYEEGWW 234

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 275 AVQDEGSQLIARAVtmAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGL---PVTVT 351
Cdd:PRK14901 235 TVQDRSAQLVAPLL--DPQPGE---VILDACAAPGGKTTHIAELMGDQG-EIWAVDRSASRLKKLQENAQRLglkSIKIL 308

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 352 VADGRDTGLETG-----FDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPH 426
Cdd:PRK14901 309 AADSRNLLELKPqwrgyFDRILLDAPCSGLGTLHRHPDARWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYATCTLH 388

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896167232 427 LRETRGIVDRAVTELPVTELSahelvapmtdvgpYPSVQMWPHRHGTDAMFFSVLRK 483
Cdd:PRK14901 389 PAENEAQIEQFLARHPDWKLE-------------PPKQKIWPHRQDGDGFFMAVLRK 432
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 45-483 1.68e-65

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: 217.43  E-value: 1.68e-65
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232   45 RKVALKVLADVREKDAYANLLLPKllkTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSdIAGPVMDVLRL-G 123
Cdd:TIGR00563   1 RSIAAQALEQLEQGQSLSNLLPPL---QQKVSDQDRALLQELCFGVLRTLSQLDWLIKKLMDRPMK-GKPRTVHYLILvG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  124 TYQLLRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTEsewvaEIapdpaTDPIGYVAMKHAHPRWiameFA 203
Cdd:TIGR00563  77 LYQLLYTRIPAHAAVAETVEGAKAIKRKGLKGLVNGVLRRFQREQE-----EL-----LAEFNALDARYLHPEW----LV 142

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  204 RALGAQAGELQQAL-AADDARPLVHLVARPGEITAEEL-----ALITGGEEGQWSPYCVRLDSGAP-GELEPVRQGLAAV 276
Cdd:TIGR00563 143 KRLQKAYPGQWQSIcEANNQRPPMWLRINRTKHSRDEWlallaEAGMKGFPHDLAPDAVRLETPAAvHALPGFEEGWVTV 222

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  277 QDEGSQLIARAvtMAPVAGEDSgrwLDLCSGPGGKSAFIGGIAAieGAKLDAVEVSATRAELVKKATT--GLPVTVTVAD 354
Cdd:TIGR00563 223 QDASAQWVATW--LAPQNEETI---LDACAAPGGKTTHILELAP--QAQVVALDIHEHRLKRVYENLKrlGLTIKAETKD 295

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  355 GRDTGL-----ETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRE 429
Cdd:TIGR00563 296 GDGRGPsqwaeNEQFDRILLDAPCSATGVIRRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATCSVLPEE 375

                         410       420       430       440       450
                  ....*....|....*....|....*....|....*....|....*....|....
gi 896167232  430 TRGIVDRAVTELPVTELSAHELVAPMTDVGpypsVQMWPHRHGTDAMFFSVLRK 483
Cdd:TIGR00563 376 NSEQIKAFLQEHPDFPFEKTGTPEQVRDGG----LQILPHAEEGDGFFYAKLIK 425
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 45-424 4.04e-65

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 216.85  E-value: 4.04e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  45 RKVALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLsDIAGPVM-DVLRLG 123
Cdd:PRK14904   5 RELALQVLQELETGERKSDTLLHRMLERSSLERNDRALATELVNGVLRYRLQLDFIISRFYHHDL-EKAAPVLkNILRLG 83

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 124 TYQLLR-TRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTES--EWVAEIapdpatDPIGYVAMKHAHPRWIAM 200
Cdd:PRK14904  84 VYQLLFlDRVPRWAAVNECVKLARKYKGEHMAKLVNGVLRNISPETISldEWLKGM------PEAERLSLLYSHPEWLLE 157

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 201 EFARALGAQAGElqQALAADDARPLVHLVARPGEITAEELALITGGEEGQWspycvrLDSGAPG--------ELEP-VRQ 271
Cdd:PRK14904 158 RWIARYGEERTE--AMLSYNNQAPLFGFRINRLKTTPEKFLAAPADASVTF------EKSGLPNfflskdfsLFEPfLKL 229

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 272 GLAAVQDEgSQLIArAVTMAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGLPVTV- 350
Cdd:PRK14904 230 GLVSVQNP-TQALA-CLLLNPQPGS---TVLDLCAAPGGKSTFMAELMQNRG-QITAVDRYPQKLEKIRSHASALGITIi 303

                        330       340       350       360       370       380       390
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 896167232 351 -TVA-DGRDTGLETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCS 424
Cdd:PRK14904 304 eTIEgDARSFSPEEQPDAILLDAPCTGTGVLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATCS 379
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
44-484 4.52e-64

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 213.51  E-value: 4.52e-64
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  44 PRKVALKVLADVREKDAYANLLLPKLLKthKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLG 123
Cdd:PRK10901   4 LRALAAAAILQVVDQGQSLSAALPALQQ--KVSDKDRALLQELCYGVLRRLPRLEWLIAQLLAKPLKGKQRIVHALLLVG 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 124 TYQLLRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTEsEWVAEIAPDPATdpigyvamKHAHPRWIAMEFA 203
Cdd:PRK10901  82 LYQLLYTRIPAHAAVDETVEAAKALKRPWAKGLVNAVLRRFQREQE-ELLAELQADPVA--------RYNHPSWLIKRLK 152

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 204 RALGAQAgelQQALAADDARPLVHLVARPGEITAEE-LALIT----GGEEGQWSPYCVRLDSGApgelePVR------QG 272
Cdd:PRK10901 153 KAYPEQW---QAILAANNQRPPMWLRVNRRHHSRDAyLALLAeagiEAFPHAVGPDAIRLETPV-----PVHqlpgfaEG 224

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 273 LAAVQDEGSQLIARAvtMAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAieGAKLDAVEVSATRAELVKK--ATTGLPVTV 350
Cdd:PRK10901 225 WVSVQDAAAQLAATL--LAPQNGE---RVLDACAAPGGKTAHILELAP--QAQVVALDIDAQRLERVREnlQRLGLKATV 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 351 TVADGRDTG-LETG--FDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHL 427
Cdd:PRK10901 298 IVGDARDPAqWWDGqpFDRILLDAPCSATGVIRRHPDIKWLRRPEDIAALAALQSEILDALWPLLKPGGTLLYATCSILP 377

                        410       420       430       440       450
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 896167232 428 RETRGIVDRAVTELPVTELSAHELVAPmtdvgpyPSVQMWPHRHGTDAMFFSVLRKN 484
Cdd:PRK10901 378 EENEQQIKAFLARHPDAELLDTGTPQQ-------PGRQLLPGEEDGDGFFYALLIKR 427
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 287-482 5.27e-55

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: 182.62  E-value: 5.27e-55
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  287 AVTMAPVAGEdsgRWLDLCSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGLPVTVTV---ADGRDTGLETG 363
Cdd:pfam01189   1 AILLAPQEGE---TILDMCAAPGGKTTHIAELMKNQG-TVVAVDINKHRLKRVAENIHRLGVTNTIilnGDGRQPDQWLG 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  364 ---FDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRGIVDRAVTE 440
Cdd:pfam01189  77 gvlFDRILLDAPCSGTGVIRRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAVIEYFLQK 156

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 896167232  441 LPVTELSAHELVAPM-TDVGPYPSVQMWPHRHGTDAMFFSVLR 482
Cdd:pfam01189 157 HPDVELVPTPLFEPVgLAIGEQPTLRLLPHTHNGDGFFIAKLR 199
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 75-446 6.12e-46

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 165.43  E-value: 6.12e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  75 LKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPlsDIAGPVMDVLRLGTYQLLRT-RVDAYAAVDTSVRAVAKvagPGA 153
Cdd:PRK14903  34 LDDKDRRFFKELVWGVVRKEELLDWYINQLLKKK--DIPPAVRVALRMGAYQLLFMnSVPDYAAVSETVKLVKN---ENF 108

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 154 RGFVNAILRKVSSktesewvaeiAPDPATdpigyVAMKHAHPRWIaMEFARALGAQAGELQqaLAADDARPL-VHLVARP 232
Cdd:PRK14903 109 KKLVNAVLRRLRT----------VPEPKE-----LHLKYSHPKWL-VNYWRSFLPEEAVLR--IMEWNQEPLpTMLRVNS 170

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 233 GEITAEELALITGGEE-----GQWSPYCV---RLDSgAPGELEPVRQGLAAVQDEGSQLIARAVTMAPvagedSGRWLDL 304
Cdd:PRK14903 171 LAITREEVIKILAEEGteavpGKHSPFSLivrKLGV-NMNDSRVIKDGLATVQGESSQIVPLLMELEP-----GLRVLDT 244

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 305 CSGPGGKSAFIGGIAAIEGaKLDAVEVSATRAELVKKATTGL---PVTVTVADGRD--TGLETGFDRILVDAPCSGLGSL 379
Cdd:PRK14903 245 CAAPGGKTTAIAELMKDQG-KILAVDISREKIQLVEKHAKRLklsSIEIKIADAERltEYVQDTFDRILVDAPCTSLGTA 323

                        330       340       350       360       370       380
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 896167232 380 RRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRGIVDRAVTELPVTEL 446
Cdd:PRK14903 324 RNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYSTCTVTKEENTEVVKRFVYEQKDAEV 390
Methyltransferase_Sun cd00620
N-terminal RNA binding domain of the methyltransferase Sun. The rRNA-specific 5-methylcytidine ...
 45-164 4.68e-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: 118.98  E-value: 4.68e-32
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  45 RKVALKVLADVREKDAYANLLLPKLLKtHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRLGT 124
Cdd:cd00620    4 RSTAAEVLRDVLQRGASLNAVLSALQK-KDKSDRDRGLATELVYGTLRWLALLDWIINPLLKKPDVGKDPDVRNLLRLGL 82

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|
gi 896167232 125 YQLLRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKV 164
Cdd:cd00620   83 YQLLYLDVPPHAAVDETVEIAKIRKDLGRAGLVNAVLRRF 122
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 287-483 8.34e-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: 114.49  E-value: 8.34e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  287 AVTMAPVAG---EDSGRWLDLCSGPGGKSAFIGGIAAIEGAKLdAVEVSATRAELVKKATTGLPVT---VTVADGRDTG- 359
Cdd:TIGR00446  58 ASSMIPPIAlepREDERVLDMAAAPGGKTTQISQLMKNKGCIV-ANEISKSRTKALISNINRMGVLntiVINADGRKFGa 136

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  360 LETGFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRGIVDRAVT 439
Cdd:TIGR00446 137 YLLKFDAILLDAPCSGEGVIRKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILR 216

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 896167232  440 ELPVTELSAHELVAPMTDVGPYPSVQ----MWPHRHGTDAMFFSVLRK 483
Cdd:TIGR00446 217 KRPDVVEEIIKGDEFFGINIGKGEVKgalrVFPQNYDCEGFFVAKLRK 264
NusB COG0781
Transcription antitermination protein NusB [Transcription];
46-171 9.84e-29

Transcription antitermination protein NusB [Transcription];


Pssm-ID: 440544 [Multi-domain]  Cd Length: 128  Bit Score: 109.85  E-value: 9.84e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  46 KVALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIE-ASSSRPLSDIAGPVMDVLRLGT 124
Cdd:COG0781    1 ELALQALYQVELSGAYANEILEEFLEDEELSEADRAFATELVYGVLRNQEELDALIApYLKDWPLERLDPVDRAILRLAA 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 896167232 125 YQLL-RTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTESE 171
Cdd:COG0781   81 YELLyLDDVPYKVAINEAVELAKKFGTEDSPKFVNGVLDKIAKELRAE 128
NusB pfam01029
NusB family; The NusB protein is involved in the regulation of rRNA biosynthesis by ...
 43-165 6.36e-26

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: 102.35  E-value: 6.36e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232   43 QPRKVALKVLADVR-------EKDAYANLLLPKLLKtHKLKGRDAAFATELTYGTLRAEGLLDAVIEA-SSSRPLSDIAG 114
Cdd:pfam01029   2 NARELALQALYQVEingsdeeEKGAYLNEALDKALE-GDLSEEDRAFATELVYGVLRNLEELDALIEKlLENWPLERLSP 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|..
gi 896167232  115 PVMDVLRLGTYQLLRT-RVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVS 165
Cdd:pfam01029  81 VDRAILRLGLYELLFLdDVPPHVAINEAVELAKKFGGEKSAKFVNGVLRNVA 132
NusB_Sun cd00447
RNA binding domain of NusB (N protein-Utilization Substance B) and Sun (also known as RrmB or ...
 45-165 5.66e-18

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: 80.09  E-value: 5.66e-18
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  45 RKVALKVLADVR-EKDAYANLLLPkLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPV-MDVLRL 122
Cdd:cd00447    3 REIAFQALYQVEiRNGISLEAVLS-ALEKLQLAKKDRPFALELVYGVLRNLPELDDIISPLLKKWLLDRLDKVdRAILRL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 896167232 123 GTYQL--LRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVS 165
Cdd:cd00447   82 LLYELyqLLYDVPPPVAINEAVELAKRFGDDDSAKFVNGVLRRIA 126
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 284-435 4.11e-14

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 74.17  E-value: 4.11e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 284 IARAVTMAPVA-----GEDSGRWLDLCSGPGGKSAfigGIAAI---EGAkLDAVEVSATRaelVK----------KATTG 345
Cdd:PRK11933  95 IQEASSMLPVAalfadDNAPQRVLDMAAAPGSKTT---QIAALmnnQGA-IVANEYSASR---VKvlhanisrcgVSNVA 167

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 346 LpvtvTVADGRDTG--LETGFDRILVDAPCSGLGSLRRRPEA--RWrkSPSDLNSLTTLQFELLSEAVRLARPGGIIVYS 421
Cdd:PRK11933 168 L----THFDGRVFGaaLPETFDAILLDAPCSGEGTVRKDPDAlkNW--SPESNLEIAATQRELIESAFHALKPGGTLVYS 241

                        170
                 ....*....|....
gi 896167232 422 TCSPHLRETRGIVD 435
Cdd:PRK11933 242 TCTLNREENQAVCL 255
Terminator_NusB cd00619
Transcription termination factor NusB (N protein-Utilization Substance B). NusB plays a key ...
 45-168 2.14e-07

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: 49.59  E-value: 2.14e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  45 RKVALKVL--ADVREKDAYANLLLPKLLKthKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDiAGPVMD--VL 120
Cdd:cd00619    5 RELAVQALyaWELAPEILAEVVSLLELLQ--YKSKKVLPFALKLVRGVLENIEEIDELIEKHLRNWSLD-RLAIVEraIL 81

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*....
gi 896167232 121 RLGTYQLLRTRVDAYAAV-DTSVRAVAKVAGPGARGFVNAILRKVSSKT 168
Cdd:cd00619   82 RLAVYELLFLPDVPHPVViNEAIELAKRFGGDDSHKFVNGVLDKIAKDL 130
nusB PRK00202
transcription antitermination factor NusB;
45-171 4.93e-07

transcription antitermination factor NusB;


Pssm-ID: 234686 [Multi-domain]  Cd Length: 137  Bit Score: 49.02  E-value: 4.93e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  45 RKVALKVL--ADVRekDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIE-ASSSRPLSDIagPVMD--V 119
Cdd:PRK00202   7 REAAVQALyqWELS--GNDIAEIIEAQLLEEQYDKADPAYFRSLVRGVVENQAELDELISpYLKDWTLERL--DPVEraI 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....
gi 896167232 120 LRLGTYQLL-RTRVDAYAAVDTSVRaVAKV-AGPGARGFVNAILRKVSSKTESE 171
Cdd:PRK00202  83 LRLALYELLfRDDVPYKVVINEAIE-LAKKfGDEDSHKFVNGVLDKIAKELRPA 135
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 300-421 2.47e-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: 2.47e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 300 RWLDLCSGPGGKSAFiggIAAIEGAKLDAVEVSATRAELVKKATTGL---PVTVTVADGRD--TGLETGFDRILVDAPCS 374
Cdd:cd02440    1 RVLDLGCGTGALALA---LASGPGARVTGVDISPVALELARKAAAALladNVEVLKGDAEElpPEADESFDVIISDPPLH 77

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 896167232 375 GLGslrrrpearwrkspsdlnsltTLQFELLSEAVRLARPGGIIVYS 421
Cdd:cd02440   78 HLV---------------------EDLARFLEEARRLLKPGGVLVLT 103
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 273-437 3.10e-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: 43.83  E-value: 3.10e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 273 LAAVQDEGSQLIARavtmapVAGEDSGRWLDLCSGPGGKSAFIggiaAIEGAKLDAVEVSATRAELVKK--ATTGLPVTV 350
Cdd:COG2226    4 VAARYDGREALLAA------LGLRPGARVLDLGCGTGRLALAL----AERGARVTGVDISPEMLELAREraAEAGLNVEF 73

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232 351 TVADGRDTGLETG-FDRILVdapCSGLGSLRRRPEArwrkspsdlnslttlqfelLSEAVRLARPGGIIVYSTCS-PHLR 428
Cdd:COG2226   74 VVGDAEDLPFPDGsFDLVIS---SFVLHHLPDPERA-------------------LAEIARVLKPGGRLVVVDFSpPDLA 131


                 ....*....
gi 896167232 429 ETRGIVDRA 437
Cdd:COG2226  132 ELEELLAEA 140
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 302-416 1.41e-04

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 40.62  E-value: 1.41e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  302 LDLCSGPGGKSAFIggiAAIEGAKLDAVEVSATRAELVKK--ATTGLPVTVTVADGRDTGLETG-FDRILvdapCSGLGS 378
Cdd:pfam13649   2 LDLGCGTGRLTLAL---ARRGGARVTGVDLSPEMLERAREraAEAGLNVEFVQGDAEDLPFPDGsFDLVV----SSGVLH 74

                          90       100       110
                  ....*....|....*....|....*....|....*...
gi 896167232  379 LRRRPEARwrkspsdlnslttlqfELLSEAVRLARPGG 416
Cdd:pfam13649  75 HLPDPDLE----------------AALREIARVLKPGG 96
PksD COG3321
Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites ...
 43-460 1.75e-03

Acyl transferase domain in polyketide synthase (PKS) enzymes [Secondary metabolites biosynthesis, transport and catabolism];


Pssm-ID: 442550 [Multi-domain]  Cd Length: 1386  Bit Score: 41.01  E-value: 1.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232   43 QPRKVALKVLADVREKDAYANLLLPKLLKTHKLKGRDAAFATELTYGTLRAEGLLDAVIEASSSRPLSDIAGPVMDVLRL 122
Cdd:COG3321   857 GRRRVPLPTYPFQREDAAAALLAAALAAALAAAAALGALLLAALAAALAAALLALAAAAAAALALAAAALAALLALVALA 936

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  123 GTYQLLRTRVDAYAAVDTSVRAVAKVAGPGARGFVNAILRKVSSKTESEWVAEIAPDPATDPIGYVAMKHAHPRWIAMEF 202
Cdd:COG3321   937 AAAAALLALAAAAAAAAAALAAAEAGALLLLAAAAAAAAAAAAAAAAAAAAAAAAAAAALAAAAALALLAAAALLLAAAA 1016

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  203 ARALGAQAGELQQALAADDARPLVHLVARPGEITAEELALITgGEEGQWSPYCVRLDSGAPGELEPVRQGLAAVQDEGSQ 282
Cdd:COG3321  1017 AAAALLALAALLAAAAAALAAAAAAAAAAAALAALAAAAAAA-AALALALAALLLLAALAELALAAAALALAAALAAAAL 1095

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  283 LIARAVTMAPVAGEDSGRWLDLCSGPGGKSAFIGGIAAIEGAKLDAVEVSATRAELVKKATTGLPVTVTVADGRDTGLET 362
Cdd:COG3321  1096 ALALAALAAALLLLALLAALALAAAAAALLALAALLAAAAAAAALAAAAAAAAALALAAAAAALAAALAAALLAAAALLL 1175

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 896167232  363 GFDRILVDAPCSGLGSLRRRPEARWRKSPSDLNSLTTLQFELLSEAVRLARPGGIIVYSTCSPHLRETRGIVDRAVTELP 442
Cdd:COG3321  1176 ALALALAAALAAALAGLAALLLAALLAALLAALLALALAALAAAAAALLAAAAAAAALALLALAAAAAAVAALAAAAAAL 1255

                         410
                  ....*....|....*...
gi 896167232  443 VTELSAHELVAPMTDVGP 460
Cdd:COG3321  1256 LAALAALALLAAAAGLAA 1273
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH