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Conserved domains on  [gi|1958709416|ref|XP_038951732|]
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tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform X7 [Rattus norvegicus]

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 1.26e-51

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: 165.31  E-value: 1.26e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 191
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|.
gi 1958709416 192 KGIGIRMTEPI 202
Cdd:cd21150    82 SGIAVEMTEPV 92
RsmB super family cl33775
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 195-299 2.05e-30

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: 119.34  E-value: 2.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 195 GIRMTEPIYLS--PSFDNvlsGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKV 272
Cdd:COG0144   211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                          90       100
                  ....*....|....*....|....*..
gi 1958709416 273 TKLKQNASLLGLHSIRAFCFDATKALK 299
Cdd:COG0144   288 KRLRENLARLGLSNVEVVVADARELLE 314
 
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 1.26e-51

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: 165.31  E-value: 1.26e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 191
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|.
gi 1958709416 192 KGIGIRMTEPI 202
Cdd:cd21150    82 SGIAVEMTEPV 92
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 195-299 2.05e-30

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: 119.34  E-value: 2.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 195 GIRMTEPIYLS--PSFDNvlsGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKV 272
Cdd:COG0144   211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                          90       100
                  ....*....|....*....|....*..
gi 1958709416 273 TKLKQNASLLGLHSIRAFCFDATKALK 299
Cdd:COG0144   288 KRLRENLARLGLSNVEVVVADARELLE 314
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 226-300 3.02e-28

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 113.10  E-value: 3.02e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958709416 226 VAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIRAFCFDATKALKL 300
Cdd:PRK14901  244 VAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADSRNLLEL 318
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 227-296 4.36e-20

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: 86.32  E-value: 4.36e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 227 AHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIRAFCFDATK 296
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ 70
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 201-297 1.85e-18

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: 85.30  E-value: 1.85e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 201 PIYLSPSFDNvlsGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRdQGEVIALDKILTKVTKLKQNAS 280
Cdd:TIGR00563 208 AVHALPGFEE---GWVTVQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQVVALDIHEHRLKRVYENLK 283

                          90
                  ....*....|....*..
gi 1958709416 281 LLGLhSIRAFCFDATKA 297
Cdd:TIGR00563 284 RLGL-TIKAETKDGDGR 299
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
113-202 4.73e-07

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 46.48  E-value: 4.73e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416  113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYsDIKGKckkgakefdgtkvFLGNGISELSRKDIFNglPDLK 192
Cdd:smart00359   2 KVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKGK 65

                           90
                   ....*....|
gi 1958709416  193 GIGIRMTEPI 202
Cdd:smart00359  66 GLAVKVRRAV 75
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 92-184 1.03e-03

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: 39.00  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416  92 LPDVLLIPMTGPRKNIerqqceVIV--GAQcgNAVLRGAHVYVPGVVSASKFMKAGDVVSVYSDIKGKckkgakefdgtk 169
Cdd:COG2016    60 FPTLRGLLKYPPEKPV------VTVdmGAV--KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK------------ 119

                          90
                  ....*....|....*
gi 1958709416 170 vFLGNGISELSRKDI 184
Cdd:COG2016   120 -PLAVGRALVDGEEM 133
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 113-152 3.48e-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: 3.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958709416 113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYS 152
Cdd:pfam01472   2 RVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVT 41
 
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 1.26e-51

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: 165.31  E-value: 1.26e-51
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYSDIKGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 191
Cdd:cd21150     2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                          90
                  ....*....|.
gi 1958709416 192 KGIGIRMTEPI 202
Cdd:cd21150    82 SGIAVEMTEPV 92
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 195-299 2.05e-30

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: 119.34  E-value: 2.05e-30
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 195 GIRMTEPIYLS--PSFDNvlsGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKV 272
Cdd:COG0144   211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                          90       100
                  ....*....|....*....|....*..
gi 1958709416 273 TKLKQNASLLGLHSIRAFCFDATKALK 299
Cdd:COG0144   288 KRLRENLARLGLSNVEVVVADARELLE 314
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 226-300 3.02e-28

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 113.10  E-value: 3.02e-28
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958709416 226 VAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIRAFCFDATKALKL 300
Cdd:PRK14901  244 VAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSIKILAADSRNLLEL 318
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
205-297 5.39e-28

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 112.58  E-value: 5.39e-28
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 205 SPSFDNvlsGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGL 284
Cdd:PRK14902  224 TDLFKD---GLITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGL 300

                          90
                  ....*....|...
gi 1958709416 285 HSIRAFCFDATKA 297
Cdd:PRK14902  301 TNIETKALDARKV 313
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 202-295 6.32e-21

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 92.43  E-value: 6.32e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 202 IYLSPSFDN----VLSGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQ 277
Cdd:PRK14904  214 FFLSKDFSLfepfLKLGLVSVQNPTQALACLLLNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRS 293

                          90
                  ....*....|....*...
gi 1958709416 278 NASLLGLHSIRAFCFDAT 295
Cdd:PRK14904  294 HASALGITIIETIEGDAR 311
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 227-296 4.36e-20

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: 86.32  E-value: 4.36e-20
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 227 AHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIRAFCFDATK 296
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ 70
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 201-297 1.85e-18

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: 85.30  E-value: 1.85e-18
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 201 PIYLSPSFDNvlsGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRdQGEVIALDKILTKVTKLKQNAS 280
Cdd:TIGR00563 208 AVHALPGFEE---GWVTVQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQVVALDIHEHRLKRVYENLK 283

                          90
                  ....*....|....*..
gi 1958709416 281 LLGLhSIRAFCFDATKA 297
Cdd:TIGR00563 284 RLGL-TIKAETKDGDGR 299
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
227-296 9.67e-17

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 80.23  E-value: 9.67e-17
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 227 AHVLDPQPGEKILDLCAAPGGKTTHIAALmRDQGEVIALDKILTKVTKLKQNASLLGLHSiRAFCFDATK 296
Cdd:PRK10901  237 ATLLAPQNGERVLDACAAPGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGDARD 304
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 212-296 2.01e-16

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 77.51  E-value: 2.01e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 212 LSGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIRAFC 291
Cdd:TIGR00446  49 LFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVIN 128


                  ....*
gi 1958709416 292 FDATK 296
Cdd:TIGR00446 129 ADGRK 133
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 209-307 4.21e-16

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 78.38  E-value: 4.21e-16
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 209 DNVLSGYIFLQNLPSTVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIR 288
Cdd:PRK14903  212 RVIKDGLATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIE 291

                          90
                  ....*....|....*....
gi 1958709416 289 AFCFDATKaLKLEVMDGVD 307
Cdd:PRK14903  292 IKIADAER-LTEYVQDTFD 309
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 112-201 1.78e-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: 67.32  E-value: 1.78e-14
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 112 CEVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYSDiKGKckkgakefdgtkvFLGNGISELSRKDIfngLPDL 191
Cdd:cd07953     1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSE-GGR-------------PLAIGVAEMSSDEM---KEEL 63

                          90
                  ....*....|
gi 1958709416 192 KGIGIRMTEP 201
Cdd:cd07953    64 KGIAVRVLHF 73
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
113-202 4.73e-07

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 46.48  E-value: 4.73e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416  113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYsDIKGKckkgakefdgtkvFLGNGISELSRKDIFNglPDLK 192
Cdd:smart00359   2 KVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKGK 65

                           90
                   ....*....|
gi 1958709416  193 GIGIRMTEPI 202
Cdd:smart00359  66 GLAVKVRRAV 75
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 212-264 5.92e-07

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 50.68  E-value: 5.92e-07
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1958709416 212 LSGYIFLQN----LPstVVAHVLDPQPGEKILDLCAAPGGKTTHIAALMRDQGEVIA 264
Cdd:PRK11933   89 LSGLFYIQEassmLP--VAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIVA 143
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 92-184 1.03e-03

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: 39.00  E-value: 1.03e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416  92 LPDVLLIPMTGPRKNIerqqceVIV--GAQcgNAVLRGAHVYVPGVVSASKFMKAGDVVSVYSDIKGKckkgakefdgtk 169
Cdd:COG2016    60 FPTLRGLLKYPPEKPV------VTVdmGAV--KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK------------ 119

                          90
                  ....*....|....*
gi 1958709416 170 vFLGNGISELSRKDI 184
Cdd:COG2016   120 -PLAVGRALVDGEEM 133
RlmE COG0293
23S rRNA U2552 (ribose-2'-O)-methylase RlmE/FtsJ [Translation, ribosomal structure and ...
 234-266 1.50e-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: 39.28  E-value: 1.50e-03
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1958709416 234 PGEKILDLCAAPGGKTTHIAALMRDQGEVIALD 266
Cdd:COG0293    50 PGMRVVDLGAAPGGWSQVAAKRVGGKGRVIALD 82
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 208-296 2.35e-03

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: 37.67  E-value: 2.35e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958709416 208 FDNVLSGYIFLQNLpstvvAHVLDPQPGEKILDLCAAPGgktTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHsI 287
Cdd:COG2226     1 FDRVAARYDGREAL-----LAALGLRPGARVLDLGCGTG---RLALALAERGARVTGVDISPEMLELARERAAEAGLN-V 71


                  ....*....
gi 1958709416 288 RAFCFDATK 296
Cdd:COG2226    72 EFVVGDAED 80
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 234-308 2.98e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 37.40  E-value: 2.98e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1958709416 234 PGEKILDLCAAPGGKTTHIAALMRDQGEVIALDKILTKVTKLKQNASLLGLHSIRAFCFDATKALKLEVMDGVDV 308
Cdd:pfam13847   3 KGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDIEELPELLEDDKFDV 77
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 113-152 3.48e-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: 3.48e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|
gi 1958709416 113 EVIVGAQCGNAVLRGAHVYVPGVVSASKFMKAGDVVSVYS 152
Cdd:pfam01472   2 RVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVT 41
rrmJ PRK11188
23S rRNA (uridine(2552)-2'-O)-methyltransferase RlmE;
233-266 7.56e-03

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


Pssm-ID: 183025  Cd Length: 209  Bit Score: 37.02  E-value: 7.56e-03
                          10        20        30
                  ....*....|....*....|....*....|....
gi 1958709416 233 QPGEKILDLCAAPGGKTTHIAALMRDQGEVIALD 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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