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Conserved domains on  [gi|1822403919|ref|XP_032822526|]
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THUMP domain-containing protein 3 isoform X2 [Petromyzon marinus]

Protein Classification

THUMP domain-containing class I SAM-dependent methyltransferase( domain architecture ID 10659626)

THUMP domain-containing class I SAM-dependent methyltransferase catalyzes the methylation of one or more specific substrates using S-adenosyl-L-methionine (SAM or AdoMet) as the methyl donor; may be an RNA methylase

CATH:  2.20.25.110
EC:  2.1.1.-
Gene Ontology:  GO:0008168|GO:1904047|GO:0003723
PubMed:  12504684|12826405|11295541
SCOP:  3000118

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
AdoMet_MTases super family cl17173
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 296-476 1.61e-50

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.).


The actual alignment was detected with superfamily member pfam01170:

Pssm-ID: 473071 [Multi-domain]  Cd Length: 184  Bit Score: 171.38  E-value: 1.61e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 296 RNITHF-GPTTLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSFHIGGDSFPMATNRSVNNVNHL--NSK 372
Cdd:pfam01170   1 RGYRPFnGPAPLKETLAAAMVNLAGWKPGDPLLDPMCGSGTILIEAALMGANIAPGKFDARVRAPLYGSDIDRRMvqGAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 373 RNSG--GRSLPVDIVQWDVCRLPLKTASVDACVTDMPFGKRMGSRRRNWDLYPACLLELARVCRPGtGRAALLTQDKKCM 450
Cdd:pfam01170  81 LNAEnaGVGDLIEFVQADAADLPLLEGSVDVIVTNPPYGIRLGSKGALEALYPEFLREAKRVLRGG-GWLVLLTAENKDF 159

                         170       180
                  ....*....|....*....|....*.
gi 1822403919 451 SKVLMQMGhlWRKAHTVWVNVGGLHA 476
Cdd:pfam01170 160 EKAARERA--WRKKKEFNVHIGGTRV 183
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 210-286 1.33e-15

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


:

Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 71.92  E-value: 1.33e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1822403919  210 VAAPEEPEELPGGDggrtlRFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFG-WKADMKNFDVEVLVNIHDQEMCVGI 286
Cdd:smart00981  10 LELIRWEKIFKEGK-----TFAVRAKRRGKNHEFTSLEVKRAIGDKLLEKTGgRKVDLKNPDVVIRVELRKDKAYLSI 82
 
Name Accession Description Interval E-value
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 296-476 1.61e-50

Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.


Pssm-ID: 395932 [Multi-domain]  Cd Length: 184  Bit Score: 171.38  E-value: 1.61e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 296 RNITHF-GPTTLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSFHIGGDSFPMATNRSVNNVNHL--NSK 372
Cdd:pfam01170   1 RGYRPFnGPAPLKETLAAAMVNLAGWKPGDPLLDPMCGSGTILIEAALMGANIAPGKFDARVRAPLYGSDIDRRMvqGAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 373 RNSG--GRSLPVDIVQWDVCRLPLKTASVDACVTDMPFGKRMGSRRRNWDLYPACLLELARVCRPGtGRAALLTQDKKCM 450
Cdd:pfam01170  81 LNAEnaGVGDLIEFVQADAADLPLLEGSVDVIVTNPPYGIRLGSKGALEALYPEFLREAKRVLRGG-GWLVLLTAENKDF 159

                         170       180
                  ....*....|....*....|....*.
gi 1822403919 451 SKVLMQMGhlWRKAHTVWVNVGGLHA 476
Cdd:pfam01170 160 EKAARERA--WRKKKEFNVHIGGTRV 183
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 300-447 2.77e-23

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: 96.56  E-value: 2.77e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 300 HFGPTTLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSfhIGGDSFPMATNRSVNNVNHLNSKRnsggrs 379
Cdd:COG1041     4 FFYPGSLDPRLARALVNLAGAKEGDTVLDPFCGTGTILIEAGLLGRRV--IGSDIDPKMVEGARENLEHYGYED------ 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1822403919 380 lpVDIVQWDVCRLPLKTASVDACVTDMPFGKRMGSRRRNW-DLYPACLLELARVCRPGtGRAALLTQDK 447
Cdd:COG1041    76 --ADVIRGDARDLPLADESVDAIVTDPPYGRSSKISGEELlELYEKALEEAARVLKPG-GRVVIVTPRD 141
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 210-286 1.33e-15

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 71.92  E-value: 1.33e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1822403919  210 VAAPEEPEELPGGDggrtlRFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFG-WKADMKNFDVEVLVNIHDQEMCVGI 286
Cdd:smart00981  10 LELIRWEKIFKEGK-----TFAVRAKRRGKNHEFTSLEVKRAIGDKLLEKTGgRKVDLKNPDVVIRVELRKDKAYLSI 82
TIGR01177 TIGR01177
putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is ...
 236-442 9.57e-15

putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is found exclusively in the Archaea. [Hypothetical proteins, Conserved]


Pssm-ID: 273486 [Multi-domain]  Cd Length: 329  Bit Score: 75.55  E-value: 9.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 236 RAGDGHSFTSMEVAREFGGAVQDHfGWKADMKNFDVEVLVNIHDQEMCVGIALT--------EESLHRRniTHFGPTTLR 307
Cdd:TIGR01177  91 RDLRGYSVDKARLERKIGAILKKK-GFKVSLRRPDIVVRVVITEDIFYLGRVLEerdkeqfiERKPDRR--PFFKPGSMD 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 308 STLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSfhIGGD-SFPMATNRSVnNVNHLNSKRNSGGRslpvdivq 386
Cdd:TIGR01177 168 PKLARAMVNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKV--IGCDiDWKMVAGARI-NLEHYGIEDFFVKR-------- 236

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1822403919 387 WDVCRLPLKTASVDACVTDMPFGKRMG-SRRRNWDLYPACLLELARVCRPGTGRAAL 442
Cdd:TIGR01177 237 GDATKLPLSSESVDAIATDPPYGRSTTaAGDGLESLYERSLEEFHEVLKSEGWIVYA 293
THUMP pfam02926
THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and ...
 211-286 8.97e-14

THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 460749  Cd Length: 143  Bit Score: 68.62  E-value: 8.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1822403919 211 AAPEEPEELPGGDGGRtlrFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFGWKADMKNFDVEVLVNIHDQEMCVGI 286
Cdd:pfam02926  69 LAKEIIKDKFKKEGET---FAVRVKRRGKNHEFTSLEINREVGKAIVEKTGLKVDLENPDIVVHVEIIKDKAYISI 141
THUMP_ThiI cd11716
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the ...
 223-281 2.40e-12

THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop pyrophosphatase domain. The N-terminal THUMP domain has been implicated in the recognition of the acceptor-stem region. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212585  Cd Length: 166  Bit Score: 65.16  E-value: 2.40e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 223 DGGRTlrFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFG-WKADMKNFDVEVLVNIHDQE 281
Cdd:cd11716    97 KKGKT--FKVRAKRADKSFPFTSMEINREVGAALLENTPdLKVDLKNPDVTIRVEIREDG 154
RlmL COG0116
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA ...
 230-339 8.10e-12

23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 439886 [Multi-domain]  Cd Length: 369  Bit Score: 66.66  E-value: 8.10e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 230 FRVTCNRAGDgHSFTSMEVAREFGGAVQDHFGWKA------DMKNFDVEVLVNIHDQEMCVGIALTEESLHRRN---ITH 300
Cdd:COG0116    90 FAVDATSVKS-KLFHSQFAALRVKDAIVDRFREKYgarpsvDEDGPDVRIHVHLLKDRATLSLDTSGESLHKRGyreAQG 168

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1822403919 301 FGPttLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVE 339
Cdd:COG0116   169 EAP--LKETLAAALLLLSGWDGDRPLVDPMCGSGTILIE 205
rlmL PRK11783
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2)) ...
 265-342 2.40e-07

bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL;


Pssm-ID: 236981 [Multi-domain]  Cd Length: 702  Bit Score: 53.65  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 265 DMKNFDVEVLVNIHDQEMCVGIALTEESLHRRNI-THFGPTTLRSTLAYGMLRLCS-PQPGDIIIDPMCGTGAIPVECGM 342
Cdd:PRK11783  131 DKEQPDIRINARLNKGEATISLDLSGESLHQRGYrQATGEAPLKENLAAAILLRSGwPQEGTPLLDPMCGSGTLLIEAAM 210
 
Name Accession Description Interval E-value
UPF0020 pfam01170
Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated ...
 296-476 1.61e-50

Putative RNA methylase family UPF0020; This domain is probably a methylase. It is associated with the THUMP domain that also occurs with RNA modification domains.


Pssm-ID: 395932 [Multi-domain]  Cd Length: 184  Bit Score: 171.38  E-value: 1.61e-50
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 296 RNITHF-GPTTLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSFHIGGDSFPMATNRSVNNVNHL--NSK 372
Cdd:pfam01170   1 RGYRPFnGPAPLKETLAAAMVNLAGWKPGDPLLDPMCGSGTILIEAALMGANIAPGKFDARVRAPLYGSDIDRRMvqGAR 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 373 RNSG--GRSLPVDIVQWDVCRLPLKTASVDACVTDMPFGKRMGSRRRNWDLYPACLLELARVCRPGtGRAALLTQDKKCM 450
Cdd:pfam01170  81 LNAEnaGVGDLIEFVQADAADLPLLEGSVDVIVTNPPYGIRLGSKGALEALYPEFLREAKRVLRGG-GWLVLLTAENKDF 159

                         170       180
                  ....*....|....*....|....*.
gi 1822403919 451 SKVLMQMGhlWRKAHTVWVNVGGLHA 476
Cdd:pfam01170 160 EKAARERA--WRKKKEFNVHIGGTRV 183
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 300-447 2.77e-23

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: 96.56  E-value: 2.77e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 300 HFGPTTLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSfhIGGDSFPMATNRSVNNVNHLNSKRnsggrs 379
Cdd:COG1041     4 FFYPGSLDPRLARALVNLAGAKEGDTVLDPFCGTGTILIEAGLLGRRV--IGSDIDPKMVEGARENLEHYGYED------ 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1822403919 380 lpVDIVQWDVCRLPLKTASVDACVTDMPFGKRMGSRRRNW-DLYPACLLELARVCRPGtGRAALLTQDK 447
Cdd:COG1041    76 --ADVIRGDARDLPLADESVDAIVTDPPYGRSSKISGEELlELYEKALEEAARVLKPG-GRVVIVTPRD 141
THUMP smart00981
The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP ...
 210-286 1.33e-15

The THUMP domain is named after after thiouridine synthases, methylases and PSUSs; The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterised RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 214952 [Multi-domain]  Cd Length: 83  Bit Score: 71.92  E-value: 1.33e-15
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1822403919  210 VAAPEEPEELPGGDggrtlRFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFG-WKADMKNFDVEVLVNIHDQEMCVGI 286
Cdd:smart00981  10 LELIRWEKIFKEGK-----TFAVRAKRRGKNHEFTSLEVKRAIGDKLLEKTGgRKVDLKNPDVVIRVELRKDKAYLSI 82
TIGR01177 TIGR01177
putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is ...
 236-442 9.57e-15

putative methyltransferase, TIGR01177 family; This family of probable methyltransferases is found exclusively in the Archaea. [Hypothetical proteins, Conserved]


Pssm-ID: 273486 [Multi-domain]  Cd Length: 329  Bit Score: 75.55  E-value: 9.57e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 236 RAGDGHSFTSMEVAREFGGAVQDHfGWKADMKNFDVEVLVNIHDQEMCVGIALT--------EESLHRRniTHFGPTTLR 307
Cdd:TIGR01177  91 RDLRGYSVDKARLERKIGAILKKK-GFKVSLRRPDIVVRVVITEDIFYLGRVLEerdkeqfiERKPDRR--PFFKPGSMD 167

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 308 STLAYGMLRLCSPQPGDIIIDPMCGTGAIPVECGMEWPRSfhIGGD-SFPMATNRSVnNVNHLNSKRNSGGRslpvdivq 386
Cdd:TIGR01177 168 PKLARAMVNLARVTEGDRVLDPFCGTGGFLIEAGLMGAKV--IGCDiDWKMVAGARI-NLEHYGIEDFFVKR-------- 236

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1822403919 387 WDVCRLPLKTASVDACVTDMPFGKRMG-SRRRNWDLYPACLLELARVCRPGTGRAAL 442
Cdd:TIGR01177 237 GDATKLPLSSESVDAIATDPPYGRSTTaAGDGLESLYERSLEEFHEVLKSEGWIVYA 293
THUMP pfam02926
THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and ...
 211-286 8.97e-14

THUMP domain; The THUMP domain is named after after thiouridine synthases, methylases and PSUSs. The THUMP domain consists of about 110 amino acid residues. The structure of ThiI reveals that the THUMP has a fold unlike that of previously characterized RNA-binding domains. It is predicted that this domain is an RNA-binding domain The THUMP domain probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 460749  Cd Length: 143  Bit Score: 68.62  E-value: 8.97e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1822403919 211 AAPEEPEELPGGDGGRtlrFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFGWKADMKNFDVEVLVNIHDQEMCVGI 286
Cdd:pfam02926  69 LAKEIIKDKFKKEGET---FAVRVKRRGKNHEFTSLEINREVGKAIVEKTGLKVDLENPDIVVHVEIIKDKAYISI 141
THUMP_ThiI cd11716
THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the ...
 223-281 2.40e-12

THUMP domain of thiamine biosynthesis protein ThiI; ThiI is an enzyme responsible for the formation of the modified base S(4)U (4-thiouridine) found at position 8 in some prokaryotic tRNAs. This modification acts as a signal for UV exposure, triggering a response that provides protection against its damaging effects. ThiI consists of an N-terminal THUMP domain, followed by an NFLD domain, and a C-terminal PP-loop pyrophosphatase domain. The N-terminal THUMP domain has been implicated in the recognition of the acceptor-stem region. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212585  Cd Length: 166  Bit Score: 65.16  E-value: 2.40e-12
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 223 DGGRTlrFRVTCNRAGDGHSFTSMEVAREFGGAVQDHFG-WKADMKNFDVEVLVNIHDQE 281
Cdd:cd11716    97 KKGKT--FKVRAKRADKSFPFTSMEINREVGAALLENTPdLKVDLKNPDVTIRVEIREDG 154
RlmL COG0116
23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA ...
 230-339 8.10e-12

23S rRNA G2445 N2-methylase RlmL [Translation, ribosomal structure and biogenesis]; 23S rRNA G2445 N2-methylase RlmL is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 439886 [Multi-domain]  Cd Length: 369  Bit Score: 66.66  E-value: 8.10e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 230 FRVTCNRAGDgHSFTSMEVAREFGGAVQDHFGWKA------DMKNFDVEVLVNIHDQEMCVGIALTEESLHRRN---ITH 300
Cdd:COG0116    90 FAVDATSVKS-KLFHSQFAALRVKDAIVDRFREKYgarpsvDEDGPDVRIHVHLLKDRATLSLDTSGESLHKRGyreAQG 168

                          90       100       110
                  ....*....|....*....|....*....|....*....
gi 1822403919 301 FGPttLRSTLAYGMLRLCSPQPGDIIIDPMCGTGAIPVE 339
Cdd:COG0116   169 EAP--LKETLAAALLLLSGWDGDRPLVDPMCGSGTILIE 205
ThiI COG0301
Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme ...
 224-284 3.41e-10

Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) [Coenzyme transport and metabolism, Translation, ribosomal structure and biogenesis]; Adenylyl- and sulfurtransferase ThiI (thiamine and tRNA 4-thiouridine biosynthesis) is part of the Pathway/BioSystem: Thiamine biosynthesis


Pssm-ID: 440070 [Multi-domain]  Cd Length: 382  Bit Score: 62.03  E-value: 3.41e-10
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1822403919 224 GGRTlrFRVTCNRAGDGHSFTSMEVAREFGGAVQDHF-GWKADMKNFDVEVLVNIHDQEMCV 284
Cdd:COG0301    99 KGKT--FKVRAKRAGKHFPFTSPELEREVGGALLENTpGLKVDLKNPDVTIRVEVRDDKAYV 158
THUMP_AdoMetMT cd11715
THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Proteins of ...
 230-289 1.66e-09

THUMP domain associated with S-adenosylmethionine-dependent methyltransferases; Proteins of this family contain an N-terminal THUMP domain and a C-terminal S-adenosylmethionine-dependent methyltransferase domain. Members have been implicated in the modification of 23S RNA m2G2445, a highly conserved modification in bacteria and in the m2G6 modification of tRNA. The THUMP domain is named after thiouridine synthases, methylases and PSUSs. The domain consists of about 110 amino acid residues. It is predicted to be an RNA-binding domain and probably functions by delivering a variety of RNA modification enzymes to their targets.


Pssm-ID: 212584  Cd Length: 152  Bit Score: 56.43  E-value: 1.66e-09
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1822403919 230 FRVTCNRAGDgHSFTSMEVAREFGGAVQDHFG-----WKADMKNFDVEVLVNIHDQEMCVGIALT 289
Cdd:cd11715    88 FAVRATRVGS-KLFHSQFAALRVKDAIVDRFRekgkrPSVDLDNPDVRIRVHLSKDRATLSLDLS 151
rlmL PRK11783
bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2)) ...
 265-342 2.40e-07

bifunctional 23S rRNA (guanine(2069)-N(7))-methyltransferase RlmK/23S rRNA (guanine(2445)-N(2))-methyltransferase RlmL;


Pssm-ID: 236981 [Multi-domain]  Cd Length: 702  Bit Score: 53.65  E-value: 2.40e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 265 DMKNFDVEVLVNIHDQEMCVGIALTEESLHRRNI-THFGPTTLRSTLAYGMLRLCS-PQPGDIIIDPMCGTGAIPVECGM 342
Cdd:PRK11783  131 DKEQPDIRINARLNKGEATISLDLSGESLHQRGYrQATGEAPLKENLAAAILLRSGwPQEGTPLLDPMCGSGTLLIEAAM 210
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 314-444 8.57e-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: 42.67  E-value: 8.57e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 314 MLRLCSPQPGDIIIDPMCGTGAIPVECGmewPRSFHIggdsfpMATNRSVNNVNHLnsKRNSGGRSLPVDIVQWDVCRLP 393
Cdd:COG2226    14 LLAALGLRPGARVLDLGCGTGRLALALA---ERGARV------TGVDISPEMLELA--RERAAEAGLNVEFVVGDAEDLP 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1822403919 394 LKTASVDACVTDMPFgkrmgsrrRNWDLYPACLLELARVCRPGtGRAALLT 444
Cdd:COG2226    83 FPDGSFDLVISSFVL--------HHLPDPERALAEIARVLKPG-GRLVVVD 124
Tan1 COG1818
tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain [Translation, ribosomal structure ...
 230-277 1.35e-04

tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain [Translation, ribosomal structure and biogenesis]; tRNA(Ser,Leu) C12 N-acetylase TAN1, contains THUMP domain is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441423  Cd Length: 162  Bit Score: 42.57  E-value: 1.35e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 1822403919 230 FRVTCNRAGdGHSFTSMEVAREFGGAVQDhfGWKADMKNFDVEVLVNI 277
Cdd:COG1818   101 FAVRCEKRG-KSKLSSREVIRAIGEAIKR--GAKVDLENPDWVVLVEI 145
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 372-436 2.57e-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: 2.57e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1822403919 372 KRNSGGRSLPVDIVQWDVCRLPLKTASVDACVTDMPFGkrmgsrRRNWDLYPACLLELARVCRPG 436
Cdd:pfam13649  37 RERAAEAGLNVEFVQGDAEDLPFPDGSFDLVVSSGVLH------HLPDPDLEAALREIARVLKPG 95
PRK08317 PRK08317
hypothetical protein; Provisional
 315-446 7.35e-03

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 38.38  E-value: 7.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1822403919 315 LRLCSPQPGDIIIDPMCGTG----AIPVECGmewPRSFHIGGDSFP----MATNRSVNNvnhlnskrnsggrSLPVDIVQ 386
Cdd:PRK08317   12 FELLAVQPGDRVLDVGCGPGndarELARRVG---PEGRVVGIDRSEamlaLAKERAAGL-------------GPNVEFVR 75

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1822403919 387 WDVCRLPLKTASVDACVTDMPFgkrmgsrrrnwdlypACLL-------ELARVCRPGtGRAALLTQD 446
Cdd:PRK08317   76 GDADGLPFPDGSFDAVRSDRVL---------------QHLEdparalaEIARVLRPG-GRVVVLDTD 126
 
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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