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Conserved domains on  [gi|2217276021|ref|XP_047280737|]
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tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X10 [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 ...
 100-370 5.23e-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: 218.34  E-value: 5.23e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 100 GIRMTEPVYLS--PSFDSvlpRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKV 177
Cdd:COG0144   211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 178 EKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQP 254
Cdd:COG0144   288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 255 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkqlqrfdpsav 334
Cdd:COG0144   356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL----------- 422

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 2217276021 335 pLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 370
Cdd:COG0144   423 -LPHRhGTD-------------------GFFIARLRK 439
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 14-107 3.20e-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: 152.99  E-value: 3.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021  14 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 92
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|....*
gi 2217276021  93 kyviRGMGIRMTEPV 107
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 ...
 100-370 5.23e-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: 218.34  E-value: 5.23e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 100 GIRMTEPVYLS--PSFDSvlpRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKV 177
Cdd:COG0144   211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 178 EKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQP 254
Cdd:COG0144   288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 255 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkqlqrfdpsav 334
Cdd:COG0144   356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL----------- 422

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 2217276021 335 pLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 370
Cdd:COG0144   423 -LPHRhGTD-------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
120-372 5.37e-63

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 207.72  E-value: 5.37e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 120 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 199
Cdd:PRK14902  231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 200 TKAvkldmvedtegePPFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYS 276
Cdd:PRK14902  311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 277 TCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLkqlqrfdpsavpLPDT-DMDslrearredmlrl 355
Cdd:PRK14902  379 TCTIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQI------------LPNDyGTD------------- 433

                         250
                  ....*....|....*..
gi 2217276021 356 ankdsiGFFIAKFVKCK 372
Cdd:PRK14902  434 ------GFFIAKLRKKG 444
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 134-368 1.51e-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: 1.51e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 134 VLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKavkldmvedteg 213
Cdd:pfam01189   3 LLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------------ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 214 ePPFLP--ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQ 288
Cdd:pfam01189  71 -PDQWLggVLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 289 VAWALTKFPCLQLQPqepqIGGEGMRGAGLSCEQLKQLqrfdpsavpLPDTDmdslrearredmlrlaNKDsiGFFIAKF 368
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 ...
 14-107 3.20e-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: 152.99  E-value: 3.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021  14 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 92
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|....*
gi 2217276021  93 kyviRGMGIRMTEPV 107
Cdd:cd21150    82 ----SGIAVEMTEPV 92
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 123-310 2.04e-41

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: 150.40  E-value: 2.04e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 123 LQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMhDQGEVIALDKIFNKVEKIKQNALLLGLnSIRAFCFDGTKA 202
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKRLGL-TIKAETKDGDGR 299

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 203 vkldmvedteGEPPFLP-ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTC 278
Cdd:TIGR00563 300 ----------GPSQWAEnEQFDRILLDAPCSATGvirRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATC 369

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2217276021 279 TITLAENEEQVAWALTKFPCLQL----QPQEPQIGG 310
Cdd:TIGR00563 370 SVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 142-276 1.73e-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: 54.74  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 142 KILDLCAAPGGKTTHIAAlmHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPES 221
Cdd:cd02440     1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2217276021 222 FDRILLDAPCSgmgqrpnmactwsvkevaSYQPLQRKLFTAAVQLLKPEGVLVYS 276
Cdd:cd02440    67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 23-85 1.05e-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: 42.08  E-value: 1.05e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2217276021  23 NAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:COG2016    84 KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK-------------PLAVGRALVDGEEM 133
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
16-107 1.66e-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: 1.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021   16 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYsDIKGKckkgakefdgtkvFLGNGISELSRKEIFSGLPelkyv 95
Cdd:smart00359   4 VVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIARIKG----- 64

                           90
                   ....*....|..
gi 2217276021   96 iRGMGIRMTEPV 107
Cdd:smart00359  65 -KGLAVKVRRAV 75
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 25-85 4.41e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.52  E-value: 4.41e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2217276021  25 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:PRK14560   89 VSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEM 136
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 16-85 4.64e-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: 4.64e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021  16 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:pfam01472   4 VVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 100-370 5.23e-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: 218.34  E-value: 5.23e-67
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 100 GIRMTEPVYLS--PSFDSvlpRYLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKV 177
Cdd:COG0144   211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 178 EKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQP 254
Cdd:COG0144   288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 255 LQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGlsCEQLkqlqrfdpsav 334
Cdd:COG0144   356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--YLRL----------- 422

                         250       260       270
                  ....*....|....*....|....*....|....*..
gi 2217276021 335 pLPDT-DMDslrearredmlrlankdsiGFFIAKFVK 370
Cdd:COG0144   423 -LPHRhGTD-------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
120-372 5.37e-63

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 207.72  E-value: 5.37e-63
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 120 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 199
Cdd:PRK14902  231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 200 TKAvkldmvedtegePPFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYS 276
Cdd:PRK14902  311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 277 TCTITLAENEEQVAWALTKFPCLQLQPQEPQIGGEGMRGAGLSCEQLkqlqrfdpsavpLPDT-DMDslrearredmlrl 355
Cdd:PRK14902  379 TCTIEKEENEEVIEAFLEEHPEFELVPLQHEKPDELVYEVKDGYLQI------------LPNDyGTD------------- 433

                         250
                  ....*....|....*..
gi 2217276021 356 ankdsiGFFIAKFVKCK 372
Cdd:PRK14902  434 ------GFFIAKLRKKG 444
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 123-308 1.10e-59

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 199.00  E-value: 1.10e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 123 LQNLP------------SA-LVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGL 189
Cdd:PRK14901  223 IRQLPgyeegwwtvqdrSAqLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGL 302

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 190 NSIRAFCFDGTKAVkldmvedteGEPPFLPESFDRILLDAPCSGMG---QRPNMacTWSV--KEVASYQPLQRKLFTAAV 264
Cdd:PRK14901  303 KSIKILAADSRNLL---------ELKPQWRGYFDRILLDAPCSGLGtlhRHPDA--RWRQtpEKIQELAPLQAELLESLA 371

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....
gi 2217276021 265 QLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLQPQEPQI 308
Cdd:PRK14901  372 PLLKPGGTLVYATCTLHPAENEAQIEQFLARHPDWKLEPPKQKI 415
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 134-368 1.51e-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: 1.51e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 134 VLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKavkldmvedteg 213
Cdd:pfam01189   3 LLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------------ 70

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 214 ePPFLP--ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCTITLAENEEQ 288
Cdd:pfam01189  71 -PDQWLggVLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 289 VAWALTKFPCLQLQPqepqIGGEGMRGAGLSCEQLKQLqrfdpsavpLPDTDmdslrearredmlrlaNKDsiGFFIAKF 368
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 ...
 14-107 3.20e-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: 152.99  E-value: 3.20e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021  14 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 92
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|....*
gi 2217276021  93 kyviRGMGIRMTEPV 107
Cdd:cd21150    82 ----SGIAVEMTEPV 92
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 124-303 1.19e-45

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 162.15  E-value: 1.19e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 124 QNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKav 203
Cdd:PRK14904  235 QNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARS-- 312

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 204 kldmvedtegeppFLPE-SFDRILLDAPCSG---MGQRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCT 279
Cdd:PRK14904  313 -------------FSPEeQPDAILLDAPCTGtgvLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATCS 379

                         170       180
                  ....*....|....*....|....
gi 2217276021 280 ITLAENEEQVAWALTKFPCLQLQP 303
Cdd:PRK14904  380 IEPEENELQIEAFLQRHPEFSAEP 403
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 123-310 2.04e-41

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: 150.40  E-value: 2.04e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 123 LQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMhDQGEVIALDKIFNKVEKIKQNALLLGLnSIRAFCFDGTKA 202
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKRLGL-TIKAETKDGDGR 299

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 203 vkldmvedteGEPPFLP-ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTC 278
Cdd:TIGR00563 300 ----------GPSQWAEnEQFDRILLDAPCSATGvirRHPDIKWLRKPRDIAELAELQSEILDAIWPLLKTGGTLVYATC 369

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 2217276021 279 TITLAENEEQVAWALTKFPCLQL----QPQEPQIGG 310
Cdd:TIGR00563 370 SVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 107-370 5.26e-41

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 145.30  E-value: 5.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 107 VYLSPSFDSVLPRYL----FLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQ 182
Cdd:TIGR00446  35 VKESPFSIGSTPEYLfgyyYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALIS 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 183 NALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPEsFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKL 259
Cdd:TIGR00446 115 NINRMGVLNTIVINADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKEL 181

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 260 FTAAVQLLKPEGVLVYSTCTITLAENEEQVAWALTKFPCLQLqpqEPQIGGEGMrGAGLSCEQLKQLQRFDPSavplpdt 339
Cdd:TIGR00446 182 IDAAIDALKPGGVLVYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF-GINIGKGEVKGALRVFPQ------- 250

                         250       260       270
                  ....*....|....*....|....*....|.
gi 2217276021 340 dmdslrearredmlrlaNKDSIGFFIAKFVK 370
Cdd:TIGR00446 251 -----------------NYDCEGFFVAKLRK 264
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
130-370 1.41e-39

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 145.33  E-value: 1.41e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 130 LVSHVLNPQPGEKILDLCAAPGGKTTHIAALmHDQGEVIALDKIFNKVEKIKQNALLLGLNSiRAFCFDGTKAvkldmve 209
Cdd:PRK10901  235 LAATLLAPQNGERVLDACAAPGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGDARDP------- 305

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 210 DT--EGEPpflpesFDRILLDAPCSGMG-----------QRPNmactwsvkEVASYQPLQRKLFTAAVQLLKPEGVLVYS 276
Cdd:PRK10901  306 AQwwDGQP------FDRILLDAPCSATGvirrhpdikwlRRPE--------DIAALAALQSEILDALWPLLKPGGTLLYA 371

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 277 TCTITLAENEEQVAWALTKFPCLQLQPQ-EPQIGGegmrgaglsceqlKQLqrfdpsavpLP-DTDMDslrearredmlr 354
Cdd:PRK10901  372 TCSILPEENEQQIKAFLARHPDAELLDTgTPQQPG-------------RQL---------LPgEEDGD------------ 417

                         250
                  ....*....|....*.
gi 2217276021 355 lankdsiGFFIAKFVK 370
Cdd:PRK10901  418 -------GFFYALLIK 426
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 115-297 3.18e-31

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 123.09  E-value: 3.18e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 115 SVLPrylflqnlPSALVSHvlNPQPgEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRA 194
Cdd:PRK11933  100 SMLP--------VAALFAD--DNAP-QRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVAL 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 195 FCFDGTkavkldmvedTEGEppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEG 271
Cdd:PRK11933  169 THFDGR----------VFGA--ALPETFDAILLDAPCSGEGtvrKDPDALKNWSPESNLEIAATQRELIESAFHALKPGG 236

                         170       180
                  ....*....|....*....|....*.
gi 2217276021 272 VLVYSTCTITLAENEEQVAWALTKFP 297
Cdd:PRK11933  237 TLVYSTCTLNREENQAVCLWLKETYP 262
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 120-295 4.63e-29

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 116.90  E-value: 4.63e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 120 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 199
Cdd:PRK14903  218 LATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADA 297

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 200 TKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAAVQLLKPEGVLVYS 276
Cdd:PRK14903  298 ERLTE------------YVQDTFDRILVDAPCTSLGtarNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYS 365

                         170       180
                  ....*....|....*....|
gi 2217276021 277 TCTITLAENEEQV-AWALTK 295
Cdd:PRK14903  366 TCTVTKEENTEVVkRFVYEQ 385
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 13-106 1.96e-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: 65.01  E-value: 1.96e-13
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021  13 CEAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEIfsglpel 92
Cdd:cd07953     1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSE-GGR-------------PLAIGVAEMSSDEM------- 59

                          90
                  ....*....|....
gi 2217276021  93 KYVIRGMGIRMTEP 106
Cdd:cd07953    60 KEELKGIAVRVLHF 73
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 142-276 1.73e-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: 54.74  E-value: 1.73e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 142 KILDLCAAPGGKTTHIAAlmHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPES 221
Cdd:cd02440     1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2217276021 222 FDRILLDAPCSgmgqrpnmactwsvkevaSYQPLQRKLFTAAVQLLKPEGVLVYS 276
Cdd:cd02440    67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 113-274 3.22e-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: 46.14  E-value: 3.22e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 113 FDSVLPRYlflqNLPSALVSHvLNPQPGEKILDLCAAPGgktTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNsI 192
Cdd:COG2226     1 FDRVAARY----DGREALLAA-LGLRPGARVLDLGCGTG---RLALALAERGARVTGVDISPEMLELARERAAEAGLN-V 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 193 RAFCFDGTkavkldmvedtegEPPFLPESFDRILldapcsgmgqrpnmaCTWSVKEVASyqplQRKLFTAAVQLLKPEGV 272
Cdd:COG2226    72 EFVVGDAE-------------DLPFPDGSFDLVI---------------SSFVLHHLPD----PERALAEIARVLKPGGR 119


                  ..
gi 2217276021 273 LV 274
Cdd:COG2226   120 LV 121
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 23-85 1.05e-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: 42.08  E-value: 1.05e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2217276021  23 NAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:COG2016    84 KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK-------------PLAVGRALVDGEEM 133
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
16-107 1.66e-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: 1.66e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021   16 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYsDIKGKckkgakefdgtkvFLGNGISELSRKEIFSGLPelkyv 95
Cdd:smart00359   4 VVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIARIKG----- 64

                           90
                   ....*....|..
gi 2217276021   96 iRGMGIRMTEPV 107
Cdd:smart00359  65 -KGLAVKVRRAV 75
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 139-278 8.62e-04

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 39.32  E-value: 8.62e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 139 PGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGlnsirafcFDGTKAVKLDMvedTEGEPPFL 218
Cdd:pfam13847   3 KGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLG--------FDNVEFEQGDI---EELPELLE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 219 PESFDRILLDapcsgmgqrpnmactwsvkEVASYQPLQRKLFTAAVQLLKPEGVLVYSTC 278
Cdd:pfam13847  72 DDKFDVVISN-------------------CVLNHIPDPDKVLQEILRVLKPGGRLIISDP 112
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 139-274 2.00e-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: 2.00e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 139 PGEKILDLCAAPGGKTThiAALMHDQGEVIALDKIFNKVEKIKQNAlllGLNSIRAfcfDGTKAVKLDMVEDTEGEPpfl 218
Cdd:pfam01728  21 PGKTVLDLGAAPGGWSQ--VALQRGAGKVVGVDLGPMQLWKPRNDP---GVTFIQG---DIRDPETLDLLEELLGRK--- 89

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 2217276021 219 pesFDRILLDApcsgmgqRPNMACTWSVKEVASYQpLQRKLFTAAVQLLKPEGVLV 274
Cdd:pfam01728  90 ---VDLVLSDG-------SPFISGNKVLDHLRSLD-LVKAALEVALELLRKGGNFV 134
RlmE COG0293
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...
 139-171 2.27e-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: 2.27e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2217276021 139 PGEKILDLCAAPGGKTTHIAALMHDQGEVIALD 171
Cdd:COG0293    50 PGMRVVDLGAAPGGWSQVAAKRVGGKGRVIALD 82
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 114-355 2.34e-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: 2.34e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 114 DSVLPRYLFLQNLPSALvshvlnpQPGEKILDLCAAPGGKTTHIAALMHDQgeVIALDkiFNK--VEKIKQNALLLGLNS 191
Cdd:COG0500     8 DELLPGLAALLALLERL-------PKGGRVLDLGCGTGRNLLALAARFGGR--VIGID--LSPeaIALARARAAKAGLGN 76

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 192 IRafcFdgtkavkldMVEDTEGEPPFLPESFDRILLDApcsgmgqrpnmactwsvkeVASYQPLQR--KLFTAAVQLLKP 269
Cdd:COG0500    77 VE---F---------LVADLAELDPLPAESFDLVVAFG-------------------VLHHLPPEEreALLRELARALKP 125

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 270 EGVLVYStctITLAENEEqvawaltkFPCLQLQPQEPQIGGEGMRGAGLSCEQLKQLQRFDpSAVPLPDTDMDSLREARR 349
Cdd:COG0500   126 GGVLLLS---ASDAAAAL--------SLARLLLLATASLLELLLLLRLLALELYLRALLAA-AATEDLRSDALLESANAL 193


                  ....*.
gi 2217276021 350 EDMLRL 355
Cdd:COG0500   194 EYLLSK 199
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 113-225 3.01e-03

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


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 38.60  E-value: 3.01e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 113 FDSVLPRYLFLQNLPSALVSHV--------LNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDkiFN----KV--E 178
Cdd:PRK00216   17 FDSIAPKYDLMNDLLSFGLHRVwrrktikwLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLD--FSegmlAVgrE 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2217276021 179 KIKQNALLLGLNSIRAfcfdgtKAVKLdmvedtegepPFLPESFDRI 225
Cdd:PRK00216   95 KLRDLGLSGNVEFVQG------DAEAL----------PFPDNSFDAV 125
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 25-85 4.41e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.52  E-value: 4.41e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2217276021  25 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:PRK14560   89 VSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEM 136
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 140-295 4.55e-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: 4.55e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 140 GEKILDLCAAPGGKTthIAALMHDQGEVIALDkIFNK-VEKIKQNALLLGLNS----IRAFCFDGTKAvkldmvEDTEGE 214
Cdd:COG1092   217 GKRVLNLFSYTGGFS--VHAAAGGAKSVTSVD-LSATaLEWAKENAALNGLDDrhefVQADAFDWLRE------LAREGE 287

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021 215 ppflpeSFDRILLDAPcsgmgqrpnmacTW--SVKEVASYQPLQRKLFTAAVQLLKPEGVLVYSTCT--ITLAENEEQVA 290
Cdd:COG1092   288 ------RFDLIILDPP------------AFakSKKDLFDAQRDYKDLNRLALKLLAPGGILVTSSCSrhFSLDLFLEILA 349


                  ....*
gi 2217276021 291 WALTK 295
Cdd:COG1092   350 RAARD 354
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 16-85 4.64e-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: 4.64e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2217276021  16 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:pfam01472   4 VVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 25-85 4.81e-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: 35.94  E-value: 4.81e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2217276021  25 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 85
Cdd:cd21154    15 VANGADVMRPGIVEADEEIKKGDIVVVVDERHGK-------------PLAVGIALMSGEEM 62
rrmJ PRK11188
23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE;
138-171 9.69e-03

23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE;


Pssm-ID: 183025  Cd Length: 209  Bit Score: 37.02  E-value: 9.69e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2217276021 138 QPGEKILDLCAAPGGKTTHIAALMHDQGEVIALD 171
Cdd:PRK11188   50 KPGMTVVDLGAAPGGWSQYAVTQIGDKGRVIACD 83
 
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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