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Conserved domains on  [gi|767959833|ref|XP_011517689|]
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tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X9 [Homo sapiens]

Protein Classification

RsmB/NOP family class I SAM-dependent RNA methyltransferase( domain architecture ID 15340246)

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:1904047|GO:0008168|GO:0003723
PubMed:  12504684|12826405
SCOP:  3000118

Graphical summary

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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 ...
 147-417 5.85e-67

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: 219.49  E-value: 5.85e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 147 GIRMTEPVYLS--PSFDSvlpRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKV 224
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 225 EKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQP 301
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 302 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkqlqrfdpsav 381
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL----------- 422

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 767959833 382 pLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 417
Cdd:COG0144  423 -LPHRhGTD-------------------GFFIARLRK 439
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 61-154 5.36e-46

PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this subfamily contain PUA domains that co-occur with SAM-dependent methyltransferase domains and may play roles as cytosine-C(5)-methyltransferases specific for tRNAs or rRNAs. Nsun6 binding to its tRNA substrates requires the presence of a 3'-CCA sequence, which is precisely recognized primarily through interactions with residues from the PUA domain, where the molecular surface of the PUA domain snugly fits onto each nucleotide residue of the CCA end. Human RNA:m5C methyltransferase NSun6 (hNSun6) plays a major role in bone metastasis and could be a valuable therapeutic target for bone metastasis and therapy-resistant tumors.


:

Pssm-ID: 409292 [Multi-domain]  Cd Length: 92  Bit Score: 153.37  E-value: 5.36e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  61 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 139
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|....*
gi 767959833 140 kyviRGMGIRMTEPV 154
Cdd:cd21150   82 ----SGIAVEMTEPV 92
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 147-417 5.85e-67

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: 219.49  E-value: 5.85e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 147 GIRMTEPVYLS--PSFDSvlpRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKV 224
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 225 EKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQP 301
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 302 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkqlqrfdpsav 381
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL----------- 422

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 767959833 382 pLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 417
Cdd:COG0144  423 -LPHRhGTD-------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
167-419 4.78e-62

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 206.95  E-value: 4.78e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 167 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 246
Cdd:PRK14902 231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 247 TKAvkldmvedtegePPFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYS 323
Cdd:PRK14902 311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 324 TCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLkqlqrfdpsavpLPDT-DMDslrearredmlrl 402
Cdd:PRK14902 379 TCTIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQI------------LPNDyGTD------------- 433

                        250
                 ....*....|....*..
gi 767959833 403 ankdsiGFFIAKFVKCK 419
Cdd:PRK14902 434 ------GFFIAKLRKKG 444
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 181-415 4.88e-51

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: 170.68  E-value: 4.88e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  181 VLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKavkldmvedteg 260
Cdd:pfam01189   3 LLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------------ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  261 ePPFLP--ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQ 335
Cdd:pfam01189  71 -PDQWLggVLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  336 VAWALTKFPCLQLQPqepqIGGEGMRGAGLSCEQLKQLqrfdpsavpLPDTDmdslrearredmlrlaNKDsiGFFIAKF 415
Cdd:pfam01189 150 IEYFLQKHPDVELVP----TPLFEPVGLAIGEQPTLRL---------LPHTH----------------NGD--GFFIAKL 198
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 61-154 5.36e-46

PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this subfamily contain PUA domains that co-occur with SAM-dependent methyltransferase domains and may play roles as cytosine-C(5)-methyltransferases specific for tRNAs or rRNAs. Nsun6 binding to its tRNA substrates requires the presence of a 3'-CCA sequence, which is precisely recognized primarily through interactions with residues from the PUA domain, where the molecular surface of the PUA domain snugly fits onto each nucleotide residue of the CCA end. Human RNA:m5C methyltransferase NSun6 (hNSun6) plays a major role in bone metastasis and could be a valuable therapeutic target for bone metastasis and therapy-resistant tumors.


Pssm-ID: 409292 [Multi-domain]  Cd Length: 92  Bit Score: 153.37  E-value: 5.36e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  61 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 139
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|....*
gi 767959833 140 kyviRGMGIRMTEPV 154
Cdd:cd21150   82 ----SGIAVEMTEPV 92
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 170-357 1.07e-40

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: 149.63  E-value: 1.07e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  170 LQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMhDQGEVIALDKIFNKVEKIKQNALLLGLnSIRAFCFDGTKA 249
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKRLGL-TIKAETKDGDGR 299

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  250 vkldmvedteGEPPFLP-ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTC 325
Cdd:TIGR00563 300 ----------GPSQWAEnEQFDRILLDAPCSATGvirRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATC 369

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 767959833  326 TITLAENEEQVAWALTKFPCLQL----QPQEPQIGG 357
Cdd:TIGR00563 370 SVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 189-323 2.44e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 54.36  E-value: 2.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 189 KILDLCAAPGGKTTHIAAlmHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPES 268
Cdd:cd02440    1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 767959833 269 FDRILLDAPCSgmgqrpnmactwsvkevaSYQPLQRKLFTAAVQLLKPEGVLVYS 323
Cdd:cd02440   67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 70-132 1.58e-04

Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441619 [Multi-domain]  Cd Length: 154  Bit Score: 41.69  E-value: 1.58e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767959833  70 NAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 132
Cdd:COG2016   84 KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK-------------PLAVGRALVDGEEM 133
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
63-154 2.04e-04

Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 39.55  E-value: 2.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833    63 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYsDIKGKckkgakefdgtkvFLGNGISELSRKEIFSGLPelkyv 142
Cdd:smart00359   4 VVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIARIKG----- 64

                           90
                   ....*....|..
gi 767959833   143 iRGMGIRMTEPV 154
Cdd:smart00359  65 -KGLAVKVRRAV 75
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 63-132 4.82e-03

PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain.


Pssm-ID: 426278 [Multi-domain]  Cd Length: 74  Bit Score: 35.54  E-value: 4.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833   63 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEI 132
Cdd:pfam01472   4 VVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 72-132 6.92e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.14  E-value: 6.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767959833  72 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 132
Cdd:PRK14560  89 VSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEM 136
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 147-417 5.85e-67

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: 219.49  E-value: 5.85e-67
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 147 GIRMTEPVYLS--PSFDSvlpRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKV 224
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 225 EKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQP 301
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 302 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkqlqrfdpsav 381
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL----------- 422

                        250       260       270
                 ....*....|....*....|....*....|....*..
gi 767959833 382 pLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 417
Cdd:COG0144  423 -LPHRhGTD-------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
167-419 4.78e-62

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 206.95  E-value: 4.78e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 167 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 246
Cdd:PRK14902 231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 247 TKAvkldmvedtegePPFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYS 323
Cdd:PRK14902 311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 324 TCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLkqlqrfdpsavpLPDT-DMDslrearredmlrl 402
Cdd:PRK14902 379 TCTIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQI------------LPNDyGTD------------- 433

                        250
                 ....*....|....*..
gi 767959833 403 ankdsiGFFIAKFVKCK 419
Cdd:PRK14902 434 ------GFFIAKLRKKG 444
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 170-355 6.18e-59

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 198.23  E-value: 6.18e-59
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 170 LQNLP------------SA-LVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGL 236
Cdd:PRK14901 223 IRQLPgyeegwwtvqdrSAqLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGL 302

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 237 NSIRAFCFDGTKAVkldmvedteGEPPFLPESFDRILLDAPCSGMG---QRPNMacTWSV--KEVASYQPLQRKLFTAAV 311
Cdd:PRK14901 303 KSIKILAADSRNLL---------ELKPQWRGYFDRILLDAPCSGLGtlhRHPDA--RWRQtpEKIQELAPLQAELLESLA 371

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....
gi 767959833 312 QLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQI 355
Cdd:PRK14901 372 PLLKPGGTLVYATCTLHPAENEAQIEQFLARHPDWKLEPPKQKI 415
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 181-415 4.88e-51

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: 170.68  E-value: 4.88e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  181 VLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKavkldmvedteg 260
Cdd:pfam01189   3 LLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------------ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  261 ePPFLP--ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQ 335
Cdd:pfam01189  71 -PDQWLggVLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  336 VAWALTKFPCLQLQPqepqIGGEGMRGAGLSCEQLKQLqrfdpsavpLPDTDmdslrearredmlrlaNKDsiGFFIAKF 415
Cdd:pfam01189 150 IEYFLQKHPDVELVP----TPLFEPVGLAIGEQPTLRL---------LPHTH----------------NGD--GFFIAKL 198
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 61-154 5.36e-46

PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this subfamily contain PUA domains that co-occur with SAM-dependent methyltransferase domains and may play roles as cytosine-C(5)-methyltransferases specific for tRNAs or rRNAs. Nsun6 binding to its tRNA substrates requires the presence of a 3'-CCA sequence, which is precisely recognized primarily through interactions with residues from the PUA domain, where the molecular surface of the PUA domain snugly fits onto each nucleotide residue of the CCA end. Human RNA:m5C methyltransferase NSun6 (hNSun6) plays a major role in bone metastasis and could be a valuable therapeutic target for bone metastasis and therapy-resistant tumors.


Pssm-ID: 409292 [Multi-domain]  Cd Length: 92  Bit Score: 153.37  E-value: 5.36e-46
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  61 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 139
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|....*
gi 767959833 140 kyviRGMGIRMTEPV 154
Cdd:cd21150   82 ----SGIAVEMTEPV 92
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 171-350 3.67e-45

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 162.15  E-value: 3.67e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 171 QNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKav 250
Cdd:PRK14904 235 QNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARS-- 312

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 251 kldmvedtegeppFLPE-SFDRILLDAPCSG---MGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCT 326
Cdd:PRK14904 313 -------------FSPEeQPDAILLDAPCTGtgvLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATCS 379

                        170       180
                 ....*....|....*....|....
gi 767959833 327 ITLAENEEQVAWALTKFPCLQLQP 350
Cdd:PRK14904 380 IEPEENELQIEAFLQRHPEFSAEP 403
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 170-357 1.07e-40

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: 149.63  E-value: 1.07e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  170 LQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMhDQGEVIALDKIFNKVEKIKQNALLLGLnSIRAFCFDGTKA 249
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKRLGL-TIKAETKDGDGR 299

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  250 vkldmvedteGEPPFLP-ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTC 325
Cdd:TIGR00563 300 ----------GPSQWAEnEQFDRILLDAPCSATGvirRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATC 369

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 767959833  326 TITLAENEEQVAWALTKFPCLQL----QPQEPQIGG 357
Cdd:TIGR00563 370 SVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 154-417 2.60e-40

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 144.53  E-value: 2.60e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  154 VYLSPSFDSVLPRYL----FLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQ 229
Cdd:TIGR00446  35 VKESPFSIGSTPEYLfgyyYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALIS 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  230 NALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPEsFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKL 306
Cdd:TIGR00446 115 NINRMGVLNTIVINADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKEL 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  307 FTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLqpqEPQIGGEGMrGAGLSCEQLKQLQRFDPSavplpdt 386
Cdd:TIGR00446 182 IDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF-GINIGKGEVKGALRVFPQ------- 250

                         250       260       270
                  ....*....|....*....|....*....|.
gi 767959833  387 dmdslrearredmlrlaNKDSIGFFIAKFVK 417
Cdd:TIGR00446 251 -----------------NYDCEGFFVAKLRK 264
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
177-417 3.91e-39

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 145.33  E-value: 3.91e-39
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 177 LVSHVLNPQPGEKILDLCAAPGGKTTHIAALmHDQGEVIALDKIFNKVEKIKQNALLLGLNSiRAFCFDGTKAvkldmve 256
Cdd:PRK10901 235 LAATLLAPQNGERVLDACAAPGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGDARDP------- 305

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 257 DT--EGEPpflpesFDRILLDAPCSGMG-----------QRPNmactwsvkEVASYQPLQRKLFTAAVQLLKPEGVLVYS 323
Cdd:PRK10901 306 AQwwDGQP------FDRILLDAPCSATGvirrhpdikwlRRPE--------DIAALAALQSEILDALWPLLKPGGTLLYA 371

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 324 TCTITLAENEEQVAWALTKFPCLQLQPQ-EPQIGGegmrgaglsceqlKQLqrfdpsavpLP-DTDMDslrearredmlr 401
Cdd:PRK10901 372 TCSILPEENEQQIKAFLARHPDAELLDTgTPQQPG-------------RQL---------LPgEEDGD------------ 417

                        250
                 ....*....|....*.
gi 767959833 402 lankdsiGFFIAKFVK 417
Cdd:PRK10901 418 -------GFFYALLIK 426
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 162-344 7.41e-31

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 123.09  E-value: 7.41e-31
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 162 SVLPrylflqnlPSALVSHvlNPQPgEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRA 241
Cdd:PRK11933 100 SMLP--------VAALFAD--DNAP-QRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVAL 168

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 242 FCFDGTkavkldmvedTEGEppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEG 318
Cdd:PRK11933 169 THFDGR----------VFGA--ALPETFDAILLDAPCSGEGtvrKDPDALKNWSPESNLEIAATQRELIESAFHALKPGG 236

                        170       180
                 ....*....|....*....|....*.
gi 767959833 319 VLVYSTCTITLAENEEQVAWALTKFP 344
Cdd:PRK11933 237 TLVYSTCTLNREENQAVCLWLKETYP 262
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 167-342 2.02e-28

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 115.74  E-value: 2.02e-28
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 167 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 246
Cdd:PRK14903 218 LATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADA 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 247 TKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYS 323
Cdd:PRK14903 298 ERLTE------------YVQDTFDRILVDAPCTSLGtarNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYS 365

                        170       180
                 ....*....|....*....|
gi 767959833 324 TCTITLAENEEQV-AWALTK 342
Cdd:PRK14903 366 TCTVTKEENTEVVkRFVYEQ 385
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 60-153 2.35e-13

PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, and a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was also found in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in regulating the expression of other genes. It has been shown that the PUA domain acts as an RNA binding domain in at least some of the proteins involved in RNA metabolism.


Pssm-ID: 409289 [Multi-domain]  Cd Length: 73  Bit Score: 64.62  E-value: 2.35e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  60 CEAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEIfsglpel 139
Cdd:cd07953    1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSE-GGR-------------PLAIGVAEMSSDEM------- 59

                         90
                 ....*....|....
gi 767959833 140 KYVIRGMGIRMTEP 153
Cdd:cd07953   60 KEELKGIAVRVLHF 73
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 189-323 2.44e-09

S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). There are at least five structurally distinct families of AdoMet-MTases, class I being the largest and most diverse. Within this class enzymes can be classified by different substrate specificities (small molecules, lipids, nucleic acids, etc.) and different target atoms for methylation (nitrogen, oxygen, carbon, sulfur, etc.).


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 54.36  E-value: 2.44e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 189 KILDLCAAPGGKTTHIAAlmHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPES 268
Cdd:cd02440    1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 767959833 269 FDRILLDAPCSgmgqrpnmactwsvkevaSYQPLQRKLFTAAVQLLKPEGVLVYS 323
Cdd:cd02440   67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 160-321 3.17e-06

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: 46.53  E-value: 3.17e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 160 FDSVLPRYlflqNLPSALVSHvLNPQPGEKILDLCAAPGgktTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNsI 239
Cdd:COG2226    1 FDRVAARY----DGREALLAA-LGLRPGARVLDLGCGTG---RLALALAERGARVTGVDISPEMLELARERAAEAGLN-V 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 240 RAFCFDGTkavkldmvedtegEPPFLPESFDRILldapcsgmgqrpnmaCTWSVKEVASyqplQRKLFTAAVQLLKPEGV 319
Cdd:COG2226   72 EFVVGDAE-------------DLPFPDGSFDLVI---------------SSFVLHHLPD----PERALAEIARVLKPGGR 119


                 ..
gi 767959833 320 LV 321
Cdd:COG2226  120 LV 121
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 70-132 1.58e-04

Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441619 [Multi-domain]  Cd Length: 154  Bit Score: 41.69  E-value: 1.58e-04
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 767959833  70 NAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 132
Cdd:COG2016   84 KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK-------------PLAVGRALVDGEEM 133
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
63-154 2.04e-04

Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 39.55  E-value: 2.04e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833    63 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYsDIKGKckkgakefdgtkvFLGNGISELSRKEIFSGLPelkyv 142
Cdd:smart00359   4 VVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIARIKG----- 64

                           90
                   ....*....|..
gi 767959833   143 iRGMGIRMTEPV 154
Cdd:smart00359  65 -KGLAVKVRRAV 75
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 186-325 1.07e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 39.32  E-value: 1.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  186 PGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGlnsirafcFDGTKAVKLDMvedTEGEPPFL 265
Cdd:pfam13847   3 KGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLG--------FDNVEFEQGDI---EELPELLE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  266 PESFDRILLDapcsgmgqrpnmactwsvkEVASYQPLQRKLFTAAVQLLKPEGVLVYSTC 325
Cdd:pfam13847  72 DDKFDVVISN-------------------CVLNHIPDPDKVLQEILRVLKPGGRLIISDP 112
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 186-321 2.21e-03

FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal sources FtsJ is a methyltransferase, but actually has no effect on cell division. FtsJ's substrate is the 23S rRNA. The 1.5 A crystal structure of FtsJ in complex with its cofactor S-adenosylmethionine revealed that FtsJ has a methyltransferase fold. This family also includes the N terminus of flaviviral NS5 protein. It has been hypothesized that the N-terminal domain of NS5 is a methyltransferase involved in viral RNA capping.


Pssm-ID: 426399  Cd Length: 179  Bit Score: 38.72  E-value: 2.21e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833  186 PGEKILDLCAAPGGKTThiAALMHDQGEVIALDKIFNKVEKIKQNAlllGLNSIRAfcfDGTKAVKLDMVEDTEGEPpfl 265
Cdd:pfam01728  21 PGKTVLDLGAAPGGWSQ--VALQRGAGKVVGVDLGPMQLWKPRNDP---GVTFIQG---DIRDPETLDLLEELLGRK--- 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 767959833  266 pesFDRILLDApcsgmgqRPNMACTWSVKEVASYQpLQRKLFTAAVQLLKPEGVLV 321
Cdd:pfam01728  90 ---VDLVLSDG-------SPFISGNKVLDHLRSLD-LVKAALEVALELLRKGGNFV 134
RlmE COG0293
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...
 186-218 2.46e-03

23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and biogenesis]; 23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440062 [Multi-domain]  Cd Length: 208  Bit Score: 38.90  E-value: 2.46e-03
                         10        20        30
                 ....*....|....*....|....*....|...
gi 767959833 186 PGEKILDLCAAPGGKTTHIAALMHDQGEVIALD 218
Cdd:COG0293   50 PGMRVVDLGAAPGGWSQVAAKRVGGKGRVIALD 82
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 161-402 2.77e-03

SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, General function prediction only];


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 38.74  E-value: 2.77e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 161 DSVLPRYLFLQNLPSALvshvlnpQPGEKILDLCAAPGGKTTHIAALMHDQgeVIALDkiFNK--VEKIKQNALLLGLNS 238
Cdd:COG0500    8 DELLPGLAALLALLERL-------PKGGRVLDLGCGTGRNLLALAARFGGR--VIGID--LSPeaIALARARAAKAGLGN 76

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 239 IRafcFdgtkavkldMVEDTEGEPPFLPESFDRILLDApcsgmgqrpnmactwsvkeVASYQPLQR--KLFTAAVQLLKP 316
Cdd:COG0500   77 VE---F---------LVADLAELDPLPAESFDLVVAFG-------------------VLHHLPPEEreALLRELARALKP 125

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 317 EGVLVYStctITLAENEEqvawaltkFPCLQLQPQEPQIGGEGMRGAGLSCEQLKQLQRFDpSAVPLPDTDMDSLREARR 396
Cdd:COG0500  126 GGVLLLS---ASDAAAAL--------SLARLLLLATASLLELLLLLRLLALELYLRALLAA-AATEDLRSDALLESANAL 193


                 ....*.
gi 767959833 397 EDMLRL 402
Cdd:COG0500  194 EYLLSK 199
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 160-272 3.46e-03

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 38.98  E-value: 3.46e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 160 FDSVLPRYLFLQNLPSALVSHV--------LNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDkiFN----KV--E 225
Cdd:PRK00216  17 FDSIAPKYDLMNDLLSFGLHRVwrrktikwLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLD--FSegmlAVgrE 94

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*..
gi 767959833 226 KIKQNALLLGLNSIRAfcfdgtKAVKLdmvedtegepPFLPESFDRI 272
Cdd:PRK00216  95 KLRDLGLSGNVEFVQG------DAEAL----------PFPDNSFDAV 125
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 63-132 4.82e-03

PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, was detected in archaeal and eukaryotic pseudouridine synthases, archaeal archaeosine synthases, a family of predicted ATPases that may be involved in RNA modification, a family of predicted archaeal and bacterial rRNA methylases. Additionally, the PUA domain was detected in a family of eukaryotic proteins that also contain a domain homologous to the translation initiation factor eIF1/SUI1; these proteins may comprise a novel type of translation factors. Unexpectedly, the PUA domain was detected also in bacterial and yeast glutamate kinases; this is compatible with the demonstrated role of these enzymes in the regulation of the expression of other genes. It is predicted that the PUA domain is an RNA binding domain.


Pssm-ID: 426278 [Multi-domain]  Cd Length: 74  Bit Score: 35.54  E-value: 4.82e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833   63 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEI 132
Cdd:pfam01472   4 VVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 187-342 5.44e-03

23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]; 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 38.62  E-value: 5.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 187 GEKILDLCAAPGGKTthIAALMHDQGEVIALDkIFNK-VEKIKQNALLLGLNS----IRAFCFDGTKAvkldmvEDTEGE 261
Cdd:COG1092  217 GKRVLNLFSYTGGFS--VHAAAGGAKSVTSVD-LSATaLEWAKENAALNGLDDrhefVQADAFDWLRE------LAREGE 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767959833 262 ppflpeSFDRILLDAPcsgmgqrpnmacTW--SVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCT--ITLAENEEQVA 337
Cdd:COG1092  288 ------RFDLIILDPP------------AFakSKKDLFDAQRDYKDLNRLALKLLAPGGILVTSSCSrhFSLDLFLEILA 349


                 ....*
gi 767959833 338 WALTK 342
Cdd:COG1092  350 RAARD 354
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 72-105 6.16e-03

PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA (PseudoUridine synthase and Archaeosine transglycosylase) domain was detected in a number of proteins involved in RNA metabolism. Members of this mostly archaeal family have not been characterized functionally; they may bind to RNA. This family includes Pyrococcus horikoshii PH0734 where the N-terminal domain may modulate the binding target of the C-terminal PUA domain using its characteristic electropositive surface.


Pssm-ID: 409296 [Multi-domain]  Cd Length: 84  Bit Score: 35.56  E-value: 6.16e-03
                         10        20        30
                 ....*....|....*....|....*....|....
gi 767959833  72 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGK 105
Cdd:cd21154   15 VANGADVMRPGIVEADEEIKKGDIVVVVDERHGK 48
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 72-132 6.92e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.14  E-value: 6.92e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 767959833  72 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 132
Cdd:PRK14560  89 VSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEM 136
 
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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