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Conserved domains on  [gi|1438183031|ref|WP_114667111|]
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MULTISPECIES: 23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD [Leuconostoc]

Protein Classification

class I SAM-dependent RNA methyltransferase( domain architecture ID 11455144)

class I SAM-dependent RNA methyltransferase catalyzes the methylation of a specific RNA substrate using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor

CATH:  2.20.25.110
EC:  2.1.1.-
PubMed:  12826405|12504684
SCOP:  3000118

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
46-490 9.76e-144

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


:

Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 416.88  E-value: 9.76e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  46 QNFPLTIKRLGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEH 125
Cdd:COG2265     1 EILELTIEDLAHGGDGVARHDGKVVFVPGALPGERVRVRVTKVKKSFARAKLVEVLEPSPDRVEPPCPHFGRCGGCQLQH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 126 MTYPAQLAFKKDVIAQALEKFQprGWTHYELRDTIGMDNPYDYRNKAQFPVRKIGDKLSVGMYKRGSHELVDLPVVHTQD 205
Cdd:COG2265    81 LSYEAQLELKQRVVREALERIG--GLPEVEVEPIIGSPEPWGYRNRARLSVRRTDGRLRLGFYARGSHELVDIDECPLLD 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 206 PATMKVIRKVAELLDKLsvsiyneDKNRGTVKTIIARVshttgdvqltfvthtdgfpgdtaliaainqalpevvgifqny 285
Cdd:COG2265   159 PALNALLPALRELLAEL-------GARRGELRHLVVRA------------------------------------------ 189
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 286 npgrtslvwgeetlklwGRDTIEETILGKTFQLSPRAFMQLNHTQMTVAYEEALTALNLTHADKLVDAYAGVGTIGLTLA 365
Cdd:COG2265   190 -----------------GRDYLTERLGGLTFRISPGSFFQVNPEQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLA 252
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 366 DKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPKWQAQGwVADALIVDPPRTGLDTALRREILRTKPEKF 445
Cdd:COG2265   253 RRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLPELLWGG-RPDVVVLDPPRAGAGPEVLEALAALGPRRI 331
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*.
gi 1438183031 446 VYISCNASTLARDLVDLAQV-YQVDYIQSIDMFPQTARWEGVVKLT 490
Cdd:COG2265   332 VYVSCNPATLARDLALLVEGgYRLEKVQPVDMFPHTHHVESVALLE 377
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
46-490 9.76e-144

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 416.88  E-value: 9.76e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  46 QNFPLTIKRLGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEH 125
Cdd:COG2265     1 EILELTIEDLAHGGDGVARHDGKVVFVPGALPGERVRVRVTKVKKSFARAKLVEVLEPSPDRVEPPCPHFGRCGGCQLQH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 126 MTYPAQLAFKKDVIAQALEKFQprGWTHYELRDTIGMDNPYDYRNKAQFPVRKIGDKLSVGMYKRGSHELVDLPVVHTQD 205
Cdd:COG2265    81 LSYEAQLELKQRVVREALERIG--GLPEVEVEPIIGSPEPWGYRNRARLSVRRTDGRLRLGFYARGSHELVDIDECPLLD 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 206 PATMKVIRKVAELLDKLsvsiyneDKNRGTVKTIIARVshttgdvqltfvthtdgfpgdtaliaainqalpevvgifqny 285
Cdd:COG2265   159 PALNALLPALRELLAEL-------GARRGELRHLVVRA------------------------------------------ 189
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 286 npgrtslvwgeetlklwGRDTIEETILGKTFQLSPRAFMQLNHTQMTVAYEEALTALNLTHADKLVDAYAGVGTIGLTLA 365
Cdd:COG2265   190 -----------------GRDYLTERLGGLTFRISPGSFFQVNPEQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLA 252
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 366 DKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPKWQAQGwVADALIVDPPRTGLDTALRREILRTKPEKF 445
Cdd:COG2265   253 RRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLPELLWGG-RPDVVVLDPPRAGAGPEVLEALAALGPRRI 331
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*.
gi 1438183031 446 VYISCNASTLARDLVDLAQV-YQVDYIQSIDMFPQTARWEGVVKLT 490
Cdd:COG2265   332 VYVSCNPATLARDLALLVEGgYRLEKVQPVDMFPHTHHVESVALLE 377
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
55-484 6.18e-142

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 414.60  E-value: 6.18e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  55 LGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEHMTYPAQLAF 134
Cdd:TIGR00479   1 LDHQGEGVARFNGKTVFVPGALPGEKAEVRVTEVKKQYARARVKKILEDSPERTTPPCPHFGQCGGCQLQHLSYELQLRS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 135 KKDVIAQALEKFQPRGWTHYELRDTIGmDNPYDYRNKAQFPV-RKIGDKLSVGMYKRGSHELVDLPVVHTQDPATMKVIR 213
Cdd:TIGR00479  81 KQQQVIALLERIGKFVSEPIEDVPTIG-DDPWGYRNKARLSLgRSPSGQLQAGFYQKGSHDIVDVKQCPVQAPALNALLP 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 214 KVAELLDKLSVSIYNEDKNRGTVKTIIARVSHTTGDVQLTFVTHTDGFPGDTALIAAINQALPEVVGIFQNYNPGRTSLV 293
Cdd:TIGR00479 160 KVRAILENFGASRYLEHKELGQARHGVLRIGRHTGELSSVDRTALERFPHKEELDLYLQPDSPDVKSICQNINPEKTNVI 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 294 WGEETLKLWGRDTIEETILGKTFQLSPRAFMQLNHTQMTVAYEEALTALNLTHADKLVDAYAGVGTIGLTLADKAGEVRG 373
Cdd:TIGR00479 240 FGEETEVIAGEMPIYDKSGDLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQAKSVVG 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 374 MEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPKWQAQGWVADALIVDPPRTGLDTALRREILRTKPEKFVYISCNAS 453
Cdd:TIGR00479 320 VEGVPESVEKAQQNAELNGIANVTFYHGTLETVLPKQPWAGNGFDKVLLDPPRKGCAAGVLRTIIKLKPERIVYVSCNPA 399
                         410       420       430
                  ....*....|....*....|....*....|..
gi 1438183031 454 TLARDL-VDLAQVYQVDYIQSIDMFPQTARWE 484
Cdd:TIGR00479 400 TLARDLeALCKAGYTIARVQPVDMFPHTGHVE 431
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
46-481 7.19e-61

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 205.78  E-value: 7.19e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  46 QNFPLTIKRLGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEH 125
Cdd:PRK13168   14 QIITVTIESLDHDGRGVARHNGKTVFIEGALPGERVEVQVTEDKKQYARAKVVRILKPSPERVTPRCPHFGVCGGCQLQH 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 126 MTYPAQLAFKKDVIAQALEKFQprGWTHYELRDTIgMDNPYDYRNKAQFPVR--KIGDKLSVGMYKRGSHELVDLPVVHT 203
Cdd:PRK13168   94 LSIDAQIASKQRALEDLLKHLA--GVEPEEVLPPI-AGPPWGYRRRARLSVRyvPKKGQLLVGFREKNSSDIVDIDQCPV 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 204 QDPATMKVIRKVAELLDKLSvsiynedknrgtvktIIARVSH---TTGDvQLTFVT--HTDGFP-GDTALIAAINQAlpe 277
Cdd:PRK13168  171 LVPPLSALLPPLRALLSSLS---------------AKRRLGHvelAQGD-NGTALVlrHLEPLSeADRAKLRAFAEQ--- 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 278 vvgifQNYNpgrtslVW----GEETLKLWGRDTIEET----ILGKTFQLSPRAFMQLNHT---QMtVAYeeALTALNLTH 346
Cdd:PRK13168  232 -----HGLQ------LYlqpkGPDLVHLLGPADAQLSyylpEFGLRLAFSPRDFIQVNAQvnqKM-VAR--ALEWLDPQP 297
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 347 ADKLVDAYAGVGTIGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPK--WQAQGwvADALIVDP 424
Cdd:PRK13168  298 GDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNGLDNVTFYHANLEEDFTDqpWALGG--FDKVLLDP 375
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1438183031 425 PRTGldtALrrEILR----TKPEKFVYISCNASTLARD---LVdlAQVYQVDYIQSIDMFPQTA 481
Cdd:PRK13168  376 PRAG---AA--EVMQalakLGPKRIVYVSCNPATLARDagvLV--EAGYRLKRAGMLDMFPHTG 432
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
127-492 1.43e-16

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 80.95  E-value: 1.43e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 127 TYPAQLAFKKDVIAQALEKFQPRGWTHYELRDTigmdnpyDYRNKAQFPVRKIGDKLSVGMYKRGSHELVdlpVVHTQDP 206
Cdd:pfam05958   1 QYDAQLAEKKSRLKALFAPFYAPDPEVFASPDK-------HYRMRAEFRIWHEGDDLYYAMFDQQTKSRI---RVDQFPA 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 207 ATmkviRKVAELLDKLSVSIYNEDKNRGTVKTIiARVSHTTGDVQLTFVTHTDgfPGDTALIAAINQALPEVVGIFQNYN 286
Cdd:pfam05958  71 AS----ELINELMPALIAALRQDPALRHKLFQV-DFLTTLSGEALVSLLYHKQ--LDDEWRQAAEALRDALRAQGLDVNL 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 287 PGR---TSLVWG----EETLKLWGRDTIEETILGktfqlsprAFMQLNHTQMTVAYEEALTALNLTHADkLVDAYAGVGT 359
Cdd:pfam05958 144 IGRarkQKIVLDqdyvDETLPVAGREFIYRQVEN--------SFTQPNAAVNIKMLEWACDVTQGSKGD-LLELYCGNGN 214
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 360 IGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEAL---------FPKWQA---QGWVADALIVDPPRT 427
Cdd:pfam05958 215 FSLALARNFRKVLATEIAKPSVAAAQYNIAANNIDNVQIIRMSAEEFtqamngvreFNRLKGidlKSYNCSTIFVDPPRA 294
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1438183031 428 GLDTALrrEILRTKPEKFVYISCNASTLARDLVDLAQVYQVDYIQSIDMFPQTARWEGVVKLTKR 492
Cdd:pfam05958 295 GLDPET--LKLVQAYPRILYISCNPETLCANLEQLSKTHRVERFALFDQFPYTHHMECGVLLEKK 357
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
46-490 9.76e-144

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 416.88  E-value: 9.76e-144
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  46 QNFPLTIKRLGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEH 125
Cdd:COG2265     1 EILELTIEDLAHGGDGVARHDGKVVFVPGALPGERVRVRVTKVKKSFARAKLVEVLEPSPDRVEPPCPHFGRCGGCQLQH 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 126 MTYPAQLAFKKDVIAQALEKFQprGWTHYELRDTIGMDNPYDYRNKAQFPVRKIGDKLSVGMYKRGSHELVDLPVVHTQD 205
Cdd:COG2265    81 LSYEAQLELKQRVVREALERIG--GLPEVEVEPIIGSPEPWGYRNRARLSVRRTDGRLRLGFYARGSHELVDIDECPLLD 158
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 206 PATMKVIRKVAELLDKLsvsiyneDKNRGTVKTIIARVshttgdvqltfvthtdgfpgdtaliaainqalpevvgifqny 285
Cdd:COG2265   159 PALNALLPALRELLAEL-------GARRGELRHLVVRA------------------------------------------ 189
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 286 npgrtslvwgeetlklwGRDTIEETILGKTFQLSPRAFMQLNHTQMTVAYEEALTALNLTHADKLVDAYAGVGTIGLTLA 365
Cdd:COG2265   190 -----------------GRDYLTERLGGLTFRISPGSFFQVNPEQAEALYAAALEWLDLTGGERVLDLYCGVGTFALPLA 252
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 366 DKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPKWQAQGwVADALIVDPPRTGLDTALRREILRTKPEKF 445
Cdd:COG2265   253 RRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLPELLWGG-RPDVVVLDPPRAGAGPEVLEALAALGPRRI 331
                         410       420       430       440
                  ....*....|....*....|....*....|....*....|....*.
gi 1438183031 446 VYISCNASTLARDLVDLAQV-YQVDYIQSIDMFPQTARWEGVVKLT 490
Cdd:COG2265   332 VYVSCNPATLARDLALLVEGgYRLEKVQPVDMFPHTHHVESVALLE 377
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
55-484 6.18e-142

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 414.60  E-value: 6.18e-142
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  55 LGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEHMTYPAQLAF 134
Cdd:TIGR00479   1 LDHQGEGVARFNGKTVFVPGALPGEKAEVRVTEVKKQYARARVKKILEDSPERTTPPCPHFGQCGGCQLQHLSYELQLRS 80
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 135 KKDVIAQALEKFQPRGWTHYELRDTIGmDNPYDYRNKAQFPV-RKIGDKLSVGMYKRGSHELVDLPVVHTQDPATMKVIR 213
Cdd:TIGR00479  81 KQQQVIALLERIGKFVSEPIEDVPTIG-DDPWGYRNKARLSLgRSPSGQLQAGFYQKGSHDIVDVKQCPVQAPALNALLP 159
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 214 KVAELLDKLSVSIYNEDKNRGTVKTIIARVSHTTGDVQLTFVTHTDGFPGDTALIAAINQALPEVVGIFQNYNPGRTSLV 293
Cdd:TIGR00479 160 KVRAILENFGASRYLEHKELGQARHGVLRIGRHTGELSSVDRTALERFPHKEELDLYLQPDSPDVKSICQNINPEKTNVI 239
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 294 WGEETLKLWGRDTIEETILGKTFQLSPRAFMQLNHTQMTVAYEEALTALNLTHADKLVDAYAGVGTIGLTLADKAGEVRG 373
Cdd:TIGR00479 240 FGEETEVIAGEMPIYDKSGDLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQAKSVVG 319
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 374 MEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPKWQAQGWVADALIVDPPRTGLDTALRREILRTKPEKFVYISCNAS 453
Cdd:TIGR00479 320 VEGVPESVEKAQQNAELNGIANVTFYHGTLETVLPKQPWAGNGFDKVLLDPPRKGCAAGVLRTIIKLKPERIVYVSCNPA 399
                         410       420       430
                  ....*....|....*....|....*....|..
gi 1438183031 454 TLARDL-VDLAQVYQVDYIQSIDMFPQTARWE 484
Cdd:TIGR00479 400 TLARDLeALCKAGYTIARVQPVDMFPHTGHVE 431
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
46-481 7.19e-61

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 205.78  E-value: 7.19e-61
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031  46 QNFPLTIKRLGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVLKIREKSPQRVKPLDEYADTVGGFELEH 125
Cdd:PRK13168   14 QIITVTIESLDHDGRGVARHNGKTVFIEGALPGERVEVQVTEDKKQYARAKVVRILKPSPERVTPRCPHFGVCGGCQLQH 93
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 126 MTYPAQLAFKKDVIAQALEKFQprGWTHYELRDTIgMDNPYDYRNKAQFPVR--KIGDKLSVGMYKRGSHELVDLPVVHT 203
Cdd:PRK13168   94 LSIDAQIASKQRALEDLLKHLA--GVEPEEVLPPI-AGPPWGYRRRARLSVRyvPKKGQLLVGFREKNSSDIVDIDQCPV 170
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 204 QDPATMKVIRKVAELLDKLSvsiynedknrgtvktIIARVSH---TTGDvQLTFVT--HTDGFP-GDTALIAAINQAlpe 277
Cdd:PRK13168  171 LVPPLSALLPPLRALLSSLS---------------AKRRLGHvelAQGD-NGTALVlrHLEPLSeADRAKLRAFAEQ--- 231
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 278 vvgifQNYNpgrtslVW----GEETLKLWGRDTIEET----ILGKTFQLSPRAFMQLNHT---QMtVAYeeALTALNLTH 346
Cdd:PRK13168  232 -----HGLQ------LYlqpkGPDLVHLLGPADAQLSyylpEFGLRLAFSPRDFIQVNAQvnqKM-VAR--ALEWLDPQP 297
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 347 ADKLVDAYAGVGTIGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEALFPK--WQAQGwvADALIVDP 424
Cdd:PRK13168  298 GDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARRNGLDNVTFYHANLEEDFTDqpWALGG--FDKVLLDP 375
                         410       420       430       440       450       460
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1438183031 425 PRTGldtALrrEILR----TKPEKFVYISCNASTLARD---LVdlAQVYQVDYIQSIDMFPQTA 481
Cdd:PRK13168  376 PRAG---AA--EVMQalakLGPKRIVYVSCNPATLARDagvLV--EAGYRLKRAGMLDMFPHTG 432
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
227-492 3.80e-37

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 138.85  E-value: 3.80e-37
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 227 YNEDKNRGTVKTIIARVSHTTGDVQLTFVTHTDgfpgdtALIAAINQALPE---------VVGIfqNYNPGRTSLVWGEE 297
Cdd:PRK03522   53 YNVARKRGELKYILLTESQSDGELMLRFVLRSE------TKLARLRRALPWlqaqlpqlkVISV--NIQPVHMAILEGEE 124
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 298 TLKLWGRDTIEETILGKTFQLSPRAFMQLNhTQMTVA-YEEA---LTALNLTHadkLVDAYAGVGTIGLTLADKAGEVRG 373
Cdd:PRK03522  125 EIFLTEQQALPERFNGVPLFIRPQSFFQTN-PAVAAQlYATArdwVRELPPRS---MWDLFCGVGGFGLHCATPGMQLTG 200
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 374 MEIVPEAVDDANDNAARNNITNAHYEVGTAEAlFPkwQAQGWVADALIVDPPRTGLDTALRREILRTKPEKFVYISCNAS 453
Cdd:PRK03522  201 IEISAEAIACAKQSAAELGLTNVQFQALDSTQ-FA--TAQGEVPDLVLVNPPRRGIGKELCDYLSQMAPRFILYSSCNAQ 277
                         250       260       270
                  ....*....|....*....|....*....|....*....
gi 1438183031 454 TLARDLVDLAQvYQVDYIQSIDMFPQTARWEGVVKLTKR 492
Cdd:PRK03522  278 TMAKDLAHLPG-YRIERVQLFDMFPHTAHYEVLTLLVRQ 315
meth_trns_rumB TIGR02085
23S rRNA (uracil-5-)-methyltransferase RumB; This family consists of RNA methyltransferases ...
168-491 5.98e-30

23S rRNA (uracil-5-)-methyltransferase RumB; This family consists of RNA methyltransferases designated RumB, formerly YbjF. Members act on 23S rRNA U747 and the equivalent position in other proteobacterial species. This family is homologous to the other 23S rRNA methyltransferase RumA and to the tRNA methyltransferase TrmA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 131140  Cd Length: 374  Bit Score: 120.33  E-value: 5.98e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 168 YRNKAQFPVRKIGDKLSVGMYKRGSH--ELVDLPVVhtqdPATMKVIRKVAE-LLDKLSVSIYNEDKNRGTVKTIIARVS 244
Cdd:TIGR02085  55 FRNKAKMVVSGSVERPILGILHRDGTplDLCDCPLY----PQSFQPVFAYLKnFIARAGLTPYNVAKKKGELKFILLTES 130
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 245 HTTGDVQLTFVTHTDG-FPGDTALIAAINQALPEVVGIFQNYNPGRTSLVWGEETLKLWGRDTIEETILGKTFQLSPRAF 323
Cdd:TIGR02085 131 ENSGQLMLRFVLRSETkLAQIRRALPWLIEQLPQLEVISVNIQPVHMAILEGEEEIFLTEQQALPERFNDVPLVIRPQSF 210
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 324 MQLNHTQMTVAYEEALTALNLTHADKLVDAYAGVGTIGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTA 403
Cdd:TIGR02085 211 FQTNPKVAAQLYATARQWVREIPVTQMWDLFCGVGGFGLHCAGPDTQLTGIEIESEAIACAQQSAQMLGLDNLSFAALDS 290
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 404 EALFpkwQAQGWVADALIVDPPRTGLDTALRREILRTKPEKFVYISCNASTLARDLVDLAQvYQVDYIQSIDMFPQTARW 483
Cdd:TIGR02085 291 AKFA---TAQMSAPELVLVNPPRRGIGKELCDYLSQMAPKFILYSSCNAQTMAKDIAELSG-YQIERVQLFDMFPHTSHY 366

                  ....*...
gi 1438183031 484 EGVVKLTK 491
Cdd:TIGR02085 367 EVLTLLVR 374
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
127-492 1.43e-16

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 80.95  E-value: 1.43e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 127 TYPAQLAFKKDVIAQALEKFQPRGWTHYELRDTigmdnpyDYRNKAQFPVRKIGDKLSVGMYKRGSHELVdlpVVHTQDP 206
Cdd:pfam05958   1 QYDAQLAEKKSRLKALFAPFYAPDPEVFASPDK-------HYRMRAEFRIWHEGDDLYYAMFDQQTKSRI---RVDQFPA 70
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 207 ATmkviRKVAELLDKLSVSIYNEDKNRGTVKTIiARVSHTTGDVQLTFVTHTDgfPGDTALIAAINQALPEVVGIFQNYN 286
Cdd:pfam05958  71 AS----ELINELMPALIAALRQDPALRHKLFQV-DFLTTLSGEALVSLLYHKQ--LDDEWRQAAEALRDALRAQGLDVNL 143
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 287 PGR---TSLVWG----EETLKLWGRDTIEETILGktfqlsprAFMQLNHTQMTVAYEEALTALNLTHADkLVDAYAGVGT 359
Cdd:pfam05958 144 IGRarkQKIVLDqdyvDETLPVAGREFIYRQVEN--------SFTQPNAAVNIKMLEWACDVTQGSKGD-LLELYCGNGN 214
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 360 IGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEAL---------FPKWQA---QGWVADALIVDPPRT 427
Cdd:pfam05958 215 FSLALARNFRKVLATEIAKPSVAAAQYNIAANNIDNVQIIRMSAEEFtqamngvreFNRLKGidlKSYNCSTIFVDPPRA 294
                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1438183031 428 GLDTALrrEILRTKPEKFVYISCNASTLARDLVDLAQVYQVDYIQSIDMFPQTARWEGVVKLTKR 492
Cdd:pfam05958 295 GLDPET--LKLVQAYPRILYISCNPETLCANLEQLSKTHRVERFALFDQFPYTHHMECGVLLEKK 357
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
123-492 1.12e-13

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 72.17  E-value: 1.12e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 123 LEHMTYPAQLAFKKDVIAQALEKFQPRGWTHYElrdtigmDNPYDYRNKAQFPVRKIGDKLSVGMYKRGSHELVdlpVVH 202
Cdd:PRK05031    6 LPPEQYEAQLAEKVARLKELFAPFSAPEPEVFR-------SPPSHYRMRAEFRIWHEGDDLYYAMFDQQTKQRI---RID 75
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 203 TQDPATMKVIRKVAELLDKLsvsiynedKNRGTVKTIIARV---SHTTGDVQLTFVTHTdgfPGDTALIAAIN---QALP 276
Cdd:PRK05031   76 QFPIASELINALMPALLAAL--------RANPVLRHKLFQVdflSTLSGEILVSLLYHK---KLDEEWEQAAKalrDALF 144
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 277 EVVGIfqnynpGR---TSLVWGeetlklwgRDTIEET--ILGKTF--QLSPRAFMQLN---HTQMTvayEEALTALNLTH 346
Cdd:PRK05031  145 NVHLI------GRsrkQKIVLD--------QDYVDERlpVAGREFiyRQVENSFTQPNaavNEKML---EWALDATKGSK 207
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 347 ADkLVDAYAGVGTIGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAE----AL-----FPKWQA---QG 414
Cdd:PRK05031  208 GD-LLELYCGNGNFTLALARNFRRVLATEISKPSVAAAQYNIAANGIDNVQIIRMSAEeftqAMngvreFNRLKGidlKS 286
                         330       340       350       360       370       380       390
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1438183031 415 WVADALIVDPPRTGLDTALRReiLRTKPEKFVYISCNASTLARDLVDLAQVYQVDYIQSIDMFPQTARWEGVVKLTKR 492
Cdd:PRK05031  287 YNFSTIFVDPPRAGLDDETLK--LVQAYERILYISCNPETLCENLETLSQTHKVERFALFDQFPYTHHMECGVLLEKK 362
TRAM pfam01938
TRAM domain; This small domain has no known function. However it may perform a nucleic acid ...
42-98 7.50e-11

TRAM domain; This small domain has no known function. However it may perform a nucleic acid binding role (Bateman A. unpublished observation).


Pssm-ID: 396497 [Multi-domain]  Cd Length: 59  Bit Score: 57.61  E-value: 7.50e-11
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 1438183031  42 VRVGQNFPLTIKRLGINGEGIGYFKR-KIVFVPGALPDEVAVVKVTEVEPKYIAAKVL 98
Cdd:pfam01938   2 RYVGQTQEVLVEGLSSNGEGIGRTDNgKVVFVPGALPGEFVEVKITKVKRNYLRGELL 59
COG3269 COG3269
Predicted RNA-binding protein, contains TRAM domain [General function prediction only];
42-98 4.28e-07

Predicted RNA-binding protein, contains TRAM domain [General function prediction only];


Pssm-ID: 442500 [Multi-domain]  Cd Length: 129  Bit Score: 48.90  E-value: 4.28e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1438183031  42 VRVGQNFPLTIKRLGINGEGIGYFKRKIVFVPGALPDEVAVVKVTEVEPKYIAAKVL 98
Cdd:COG3269    70 VEEGEEYEVEIEDIGKKGDGIARVEGFVIFVPGAEVGDRVKVKITKVKRNFAFAEVV 126
PRK14968 PRK14968
putative methyltransferase; Provisional
348-400 9.34e-05

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 43.35  E-value: 9.34e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 1438183031 348 DKLVDAYAGVGTIGLTLADKAGEVRGMEIVPEAVDDANDNAARNNITNAHYEV 400
Cdd:PRK14968   25 DRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNNGVEV 77
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
336-397 7.79e-04

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 41.30  E-value: 7.79e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1438183031 336 EEALTALNLTHADKLVDAYAGVGTIGLTLADKAGEVRGM--EIVPEAVDDANDNAARNNITNAH 397
Cdd:PRK09328   98 EWALEALLLKEPLRVLDLGTGSGAIALALAKERPDAEVTavDISPEALAVARRNAKHGLGARVE 161
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
341-395 8.94e-04

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 40.90  E-value: 8.94e-04
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1438183031 341 ALNLTHADKLVDAYAGVGTIGLTLADKAGEVR--GMEIVPEAVDDANDNAARNNITN 395
Cdd:COG4123    32 FAPVKKGGRVLDLGTGTGVIALMLAQRSPGARitGVEIQPEAAELARRNVALNGLED 88
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
347-406 1.67e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 38.94  E-value: 1.67e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1438183031 347 ADKLVDAYAGVGTIGLTLADKAG---EVRGMEIVPEAVDDANDNAARNNITNAHYEVGTAEAL 406
Cdd:pfam13847   4 GMRVLDLGCGTGHLSFELAEELGpnaEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDIEEL 66
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
339-397 3.30e-03

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 38.63  E-value: 3.30e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 1438183031 339 LTALNLTHADKLVDAYAGVGTIGLTLADKAGEVR--GMEIVPEAVDDANDNAARNNITNAH 397
Cdd:COG2813    42 LEHLPEPLGGRVLDLGCGYGVIGLALAKRNPEARvtLVDVNARAVELARANAAANGLENVE 102
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
339-443 4.52e-03

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 37.96  E-value: 4.52e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1438183031 339 LTALNLTHADKLVDAYAGVGTIGLTLADKAGEVR--GMEIVPEAVDDANDNAARNNITNAHYEVGTA-EALFPKwqaqgw 415
Cdd:pfam05175  24 LEHLPKDLSGKVLDLGCGAGVLGAALAKESPDAEltMVDINARALESARENLAANGLENGEVVASDVySGVEDG------ 97
                          90       100       110
                  ....*....|....*....|....*....|.
gi 1438183031 416 VADALIVDPP-RTGLDTALR--REILRTKPE 443
Cdd:pfam05175  98 KFDLIISNPPfHAGLATTYNvaQRFIADAKR 128
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

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