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Conserved domains on  [gi|2462517677|ref|XP_054221102|]
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tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X7 [Homo sapiens]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 113-202 3.74e-48

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: 158.00  E-value: 3.74e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 113 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 191
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|.
gi 2462517677 192 KGMGIRMTEPV 202
Cdd:cd21150    82 SGIAVEMTEPV 92
RsmB super family cl33775
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 190-358 3.26e-41

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


The actual alignment was detected with superfamily member COG0144:

Pssm-ID: 439914 [Multi-domain]  Cd Length: 441  Bit Score: 150.16  E-value: 3.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 190 ELKGMGIRmTEPVYLSPsfDSV-LPRYLFLQNLP-------------SALVSHVLNPQPGEKILDLCAAPGGKTTHIAAL 255
Cdd:COG0144   194 RLAEEGIE-AEPTPLSP--DGLrLEGPGPVTALPgfreglfsvqdeaSQLVALLLDPKPGERVLDLCAAPGGKTLHLAEL 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 256 MHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QR 332
Cdd:COG0144   271 MGNKGRVVAVDISEHRLKRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRH 338

                         170       180
                  ....*....|....*....|....*.
gi 2462517677 333 PNMACTWSVKEVASYQPLQRKLFTAV 358
Cdd:COG0144   339 PDIKWRRTPEDIAELAALQRELLDAA 364
 
Name Accession Description Interval E-value
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 113-202 3.74e-48

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: 158.00  E-value: 3.74e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 113 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 191
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|.
gi 2462517677 192 KGMGIRMTEPV 202
Cdd:cd21150    82 SGIAVEMTEPV 92
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 190-358 3.26e-41

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: 150.16  E-value: 3.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 190 ELKGMGIRmTEPVYLSPsfDSV-LPRYLFLQNLP-------------SALVSHVLNPQPGEKILDLCAAPGGKTTHIAAL 255
Cdd:COG0144   194 RLAEEGIE-AEPTPLSP--DGLrLEGPGPVTALPgfreglfsvqdeaSQLVALLLDPKPGERVLDLCAAPGGKTLHLAEL 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 256 MHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QR 332
Cdd:COG0144   271 MGNKGRVVAVDISEHRLKRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRH 338

                         170       180
                  ....*....|....*....|....*.
gi 2462517677 333 PNMACTWSVKEVASYQPLQRKLFTAV 358
Cdd:COG0144   339 PDIKWRRTPEDIAELAALQRELLDAA 364
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
215-359 1.55e-40

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 148.40  E-value: 1.55e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 215 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 294
Cdd:PRK14902  231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517677 295 TKAvkldmvedtegePPFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAVC 359
Cdd:PRK14902  311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVA 366
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 229-357 1.45e-31

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: 118.30  E-value: 1.45e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 229 VLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKavkldmvedteg 308
Cdd:pfam01189   3 LLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------------ 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462517677 309 ePPFLP--ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTA 357
Cdd:pfam01189  71 -PDQWLggVLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSA 123
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 218-358 6.26e-29

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: 116.12  E-value: 6.26e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 218 LQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMhDQGEVIALDKIFNKVEKIKQNALLLGLnSIRAFCFDGTKA 297
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKRLGL-TIKAETKDGDGR 299

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517677 298 vkldmvedteGEPPFLP-ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAV 358
Cdd:TIGR00563 300 ----------GPSQWAEnEQFDRILLDAPCSATGvirRHPDIKWLRKPRDIAELAELQSEILDAI 354
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 237-333 3.45e-06

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


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 45.50  E-value: 3.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 237 KILDLCAAPGGKTTHIAAlmHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPES 316
Cdd:cd02440     1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                          90
                  ....*....|....*..
gi 2462517677 317 FDRILLDAPCSGMGQRP 333
Cdd:cd02440    67 FDVIISDPPLHHLVEDL 83
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
115-202 1.68e-05

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 42.63  E-value: 1.68e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677  115 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYsDIKGKckkgakefdgtkvFLGNGISELSRKEIFSglPELKGM 194
Cdd:smart00359   4 VVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKGKGL 67


                   ....*...
gi 2462517677  195 GIRMTEPV 202
Cdd:smart00359  68 AVKVRRAV 75
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 122-184 1.67e-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: 1.67e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517677 122 NAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 184
Cdd:COG2016    84 KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK-------------PLAVGRALVDGEEM 133
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 124-184 6.84e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 36.75  E-value: 6.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517677 124 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 184
Cdd:PRK14560   89 VSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEM 136
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 115-184 7.42e-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: 34.77  E-value: 7.42e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 115 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEI 184
Cdd:pfam01472   4 VVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
 
Name Accession Description Interval E-value
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 113-202 3.74e-48

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: 158.00  E-value: 3.74e-48
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 113 EAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKEIFSGLPEL 191
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|.
gi 2462517677 192 KGMGIRMTEPV 202
Cdd:cd21150    82 SGIAVEMTEPV 92
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 190-358 3.26e-41

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: 150.16  E-value: 3.26e-41
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 190 ELKGMGIRmTEPVYLSPsfDSV-LPRYLFLQNLP-------------SALVSHVLNPQPGEKILDLCAAPGGKTTHIAAL 255
Cdd:COG0144   194 RLAEEGIE-AEPTPLSP--DGLrLEGPGPVTALPgfreglfsvqdeaSQLVALLLDPKPGERVLDLCAAPGGKTLHLAEL 270

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 256 MHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAVKldmvedtegeppFLPESFDRILLDAPCSGMG---QR 332
Cdd:COG0144   271 MGNKGRVVAVDISEHRLKRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRH 338

                         170       180
                  ....*....|....*....|....*.
gi 2462517677 333 PNMACTWSVKEVASYQPLQRKLFTAV 358
Cdd:COG0144   339 PDIKWRRTPEDIAELAALQRELLDAA 364
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
215-359 1.55e-40

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 148.40  E-value: 1.55e-40
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 215 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 294
Cdd:PRK14902  231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2462517677 295 TKAvkldmvedtegePPFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAVC 359
Cdd:PRK14902  311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVA 366
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 218-358 6.71e-38

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 140.83  E-value: 6.71e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 218 LQNLP------------SA-LVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGL 284
Cdd:PRK14901  223 IRQLPgyeegwwtvqdrSAqLVAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGL 302

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2462517677 285 NSIRAFCFDGTKAVkldmvedteGEPPFLPESFDRILLDAPCSGMG---QRPNMacTWSV--KEVASYQPLQRKLFTAV 358
Cdd:PRK14901  303 KSIKILAADSRNLL---------ELKPQWRGYFDRILLDAPCSGLGtlhRHPDA--RWRQtpEKIQELAPLQAELLESL 370
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 229-357 1.45e-31

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: 118.30  E-value: 1.45e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 229 VLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKavkldmvedteg 308
Cdd:pfam01189   3 LLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------------ 70

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2462517677 309 ePPFLP--ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTA 357
Cdd:pfam01189  71 -PDQWLggVLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSA 123
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 219-354 6.84e-31

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 122.09  E-value: 6.84e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 219 QNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKav 298
Cdd:PRK14904  235 QNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARS-- 312

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 299 kldmvedtegeppFLPE-SFDRILLDAPCSG---MGQRPNMACTWSVKEVASYQPLQRKL 354
Cdd:PRK14904  313 -------------FSPEeQPDAILLDAPCTGtgvLGRRAELRWKLTPEKLAELVGLQAEL 359
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 218-358 6.26e-29

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: 116.12  E-value: 6.26e-29
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 218 LQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMhDQGEVIALDKIFNKVEKIKQNALLLGLnSIRAFCFDGTKA 297
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELA-PQAQVVALDIHEHRLKRVYENLKRLGL-TIKAETKDGDGR 299

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2462517677 298 vkldmvedteGEPPFLP-ESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKLFTAV 358
Cdd:TIGR00563 300 ----------GPSQWAEnEQFDRILLDAPCSATGvirRHPDIKWLRKPRDIAELAELQSEILDAI 354
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 202-361 1.89e-23

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 97.92  E-value: 1.89e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 202 VYLSPSFDSVLPRYL----FLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQ 277
Cdd:TIGR00446  35 VKESPFSIGSTPEYLfgyyYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALIS 114

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 278 NALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPEsFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKL 354
Cdd:TIGR00446 115 NINRMGVLNTIVINADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKEL 181

                         170
                  ....*....|..
gi 2462517677 355 ----FTAV-CGG 361
Cdd:TIGR00446 182 idaaIDALkPGG 193
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
225-357 2.45e-23

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 100.26  E-value: 2.45e-23
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 225 LVSHVLNPQPGEKILDLCAAPGGKTTHIAALmHDQGEVIALDKIFNKVEKIKQNALLLGLNSiRAFCFDGTKAvkldmve 304
Cdd:PRK10901  235 LAATLLAPQNGERVLDACAAPGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGDARDP------- 305

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 2462517677 305 DT--EGEPpflpesFDRILLDAPCSGMG-----------QRPNmactwsvkEVASYQPLQRKLFTA 357
Cdd:PRK10901  306 AQwwDGQP------FDRILLDAPCSATGvirrhpdikwlRRPE--------DIAALAALQSEILDA 357
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 215-330 2.57e-19

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 88.78  E-value: 2.57e-19
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 215 YLFLQNLPSALVSHVLNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDG 294
Cdd:PRK14903  218 LATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADA 297

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 2462517677 295 TKAVKldmvedtegeppFLPESFDRILLDAPCSGMG 330
Cdd:PRK14903  298 ERLTE------------YVQDTFDRILVDAPCTSLG 321
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 210-363 3.47e-16

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 79.57  E-value: 3.47e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 210 SVLPrylflqnlPSALVSHvlNPQPgEKILDLCAAPGGKTTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRA 289
Cdd:PRK11933  100 SMLP--------VAALFAD--DNAP-QRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVAL 168

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 290 FCFDGTkavkldmvedTEGEppFLPESFDRILLDAPCSGMG---QRPNMACTWSVKEVASYQPLQRKL----FTAVCGGG 362
Cdd:PRK11933  169 THFDGR----------VFGA--ALPETFDAILLDAPCSGEGtvrKDPDALKNWSPESNLEIAATQRELiesaFHALKPGG 236


                  .
gi 2462517677 363 S 363
Cdd:PRK11933  237 T 237
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 112-201 1.97e-14

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: 67.71  E-value: 1.97e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 112 CEAIVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEIfsgLPEL 191
Cdd:cd07953     1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSE-GGR-------------PLAIGVAEMSSDEM---KEEL 63

                          90
                  ....*....|
gi 2462517677 192 KGMGIRMTEP 201
Cdd:cd07953    64 KGIAVRVLHF 73
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 237-333 3.45e-06

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


Pssm-ID: 100107 [Multi-domain]  Cd Length: 107  Bit Score: 45.50  E-value: 3.45e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 237 KILDLCAAPGGKTTHIAAlmHDQGEVIALDKIFNKVEKIKQNALLLGLNSIRAFCFDGTKAvkldmvedtegePPFLPES 316
Cdd:cd02440     1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                          90
                  ....*....|....*..
gi 2462517677 317 FDRILLDAPCSGMGQRP 333
Cdd:cd02440    67 FDVIISDPPLHHLVEDL 83
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
115-202 1.68e-05

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 42.63  E-value: 1.68e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677  115 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYsDIKGKckkgakefdgtkvFLGNGISELSRKEIFSglPELKGM 194
Cdd:smart00359   4 VVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKGKGL 67


                   ....*...
gi 2462517677  195 GIRMTEPV 202
Cdd:smart00359  68 AVKVRRAV 75
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 208-322 1.75e-05

Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG is part of the Pathway/BioSystem: Biotin biosynthesis


Pssm-ID: 441828 [Multi-domain]  Cd Length: 143  Bit Score: 44.21  E-value: 1.75e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 208 FDSVLPRYlflqNLPSALVSHvLNPQPGEKILDLCAAPGgktTHIAALMHDQGEVIALDKIFNKVEKIKQNALLLGLNsI 287
Cdd:COG2226     1 FDRVAARY----DGREALLAA-LGLRPGARVLDLGCGTG---RLALALAERGARVTGVDISPEMLELARERAAEAGLN-V 71

                          90       100       110
                  ....*....|....*....|....*....|....*
gi 2462517677 288 RAFCFDGTkavkldmvedtegEPPFLPESFDRILL 322
Cdd:COG2226    72 EFVVGDAE-------------DLPFPDGSFDLVIS 93
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 122-184 1.67e-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: 1.67e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2462517677 122 NAVLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 184
Cdd:COG2016    84 KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK-------------PLAVGRALVDGEEM 133
RlmE COG0293
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...
 234-266 2.05e-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: 2.05e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 2462517677 234 PGEKILDLCAAPGGKTTHIAALMHDQGEVIALD 266
Cdd:COG0293    50 PGMRVVDLGAAPGGWSQVAAKRVGGKGRVIALD 82
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 208-320 2.91e-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: 2.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 208 FDSVLPRYLFLQNLPSALVSHV--------LNPQPGEKILDLCAAPGGKTTHIAALMHDQGEVIALDkiFN----KV--E 273
Cdd:PRK00216   17 FDSIAPKYDLMNDLLSFGLHRVwrrktikwLGVRPGDKVLDLACGTGDLAIALAKAVGKTGEVVGLD--FSegmlAVgrE 94

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*..
gi 2462517677 274 KIKQNALLLGLNSIRAfcfdgtKAVKLdmvedtegepPFLPESFDRI 320
Cdd:PRK00216   95 KLRDLGLSGNVEFVQG------DAEAL----------PFPDNSFDAV 125
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 124-184 6.84e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 36.75  E-value: 6.84e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 2462517677 124 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGKckkgakefdgtkvFLGNGISELSRKEI 184
Cdd:PRK14560   89 VSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEM 136
PUA_MJ1432-like cd21154
PUA RNA-binding domain of MJ1432, TA1423, PH0734, and similar proteins; The RNA-binding PUA ...
 124-157 7.02e-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: 35.17  E-value: 7.02e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2462517677 124 VLRGAHVYAPGIVSASQFMKAGDVISVYSDIKGK 157
Cdd:cd21154    15 VANGADVMRPGIVEADEEIKKGDIVVVVDERHGK 48
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 115-184 7.42e-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: 34.77  E-value: 7.42e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2462517677 115 IVGAQCGNAVLRGAHVYAPGIVSASQFMKAGDVISVYSDiKGKckkgakefdgtkvFLGNGISELSRKEI 184
Cdd:pfam01472   4 VVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
rrmJ PRK11188
23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE;
233-266 8.26e-03

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


Pssm-ID: 183025  Cd Length: 209  Bit Score: 37.40  E-value: 8.26e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 2462517677 233 QPGEKILDLCAAPGGKTTHIAALMHDQGEVIALD 266
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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