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Conserved domains on  [gi|260099664|ref|NP_001159415|]
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tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform c [Mus musculus]

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 ...
 144-414 3.19e-66

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: 217.95  E-value: 3.19e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 144 GIRMTEPIYLS--PSFDNvlpSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKV 221
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 222 NKLKQNASLLGLHSIRAFCFDATKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQP 298
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 299 LQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVAWALRTFPCLQLQPQEPQIGGEGMVGAGltleqlkqLQRFDPSVv 378
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--------YLRLLPHR- 426

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 260099664 379 plQNMDtdslgearredmiwlankdciGFFIAKFLK 414
Cdd:COG0144  427 --HGTD---------------------GFFIARLRK 439
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 62-151 3.03e-50

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: 164.54  E-value: 3.03e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  62 EVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 140
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|.
gi 260099664 141 KGIGIRMTEPI 151
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 ...
 144-414 3.19e-66

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: 217.95  E-value: 3.19e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 144 GIRMTEPIYLS--PSFDNvlpSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKV 221
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 222 NKLKQNASLLGLHSIRAFCFDATKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQP 298
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 299 LQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVAWALRTFPCLQLQPQEPQIGGEGMVGAGltleqlkqLQRFDPSVv 378
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--------YLRLLPHR- 426

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 260099664 379 plQNMDtdslgearredmiwlankdciGFFIAKFLK 414
Cdd:COG0144  427 --HGTD---------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
164-414 6.06e-62

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 206.57  E-value: 6.06e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 164 YIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDA 243
Cdd:PRK14902 231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 244 TKAlkldttdgieggPPFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYS 320
Cdd:PRK14902 311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 321 TCTITLAENEEQVAWALRTFPCLQLQPQEPqiggegmvgaGLTLEQLKQLQRFDPSVVPLQNmDTDslgearredmiwla 400
Cdd:PRK14902 379 TCTIEKEENEEVIEAFLEEHPEFELVPLQH----------EKPDELVYEVKDGYLQILPNDY-GTD-------------- 433

                        250
                 ....*....|....
gi 260099664 401 nkdciGFFIAKFLK 414
Cdd:PRK14902 434 -----GFFIAKLRK 442
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 176-413 3.06e-52

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: 173.76  E-value: 3.06e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  176 AHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKalkldtTDGI 255
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------PDQW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  256 EGGppflpESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQ 332
Cdd:pfam01189  75 LGG-----VLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  333 VAWALRTFPCLQLQPqepqIGGEGMVGAGLTLEQLKQlqrfdpsVVPLQNmdtdslgearredmiwlaNKDciGFFIAKF 412
Cdd:pfam01189 150 IEYFLQKHPDVELVP----TPLFEPVGLAIGEQPTLR-------LLPHTH------------------NGD--GFFIAKL 198


                  .
gi 260099664  413 L 413
Cdd:pfam01189 199 R 199
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 62-151 3.03e-50

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: 164.54  E-value: 3.03e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  62 EVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 140
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|.
gi 260099664 141 KGIGIRMTEPI 151
Cdd:cd21150   82 SGIAVEMTEPV 92
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 161-414 3.97e-47

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 162.64  E-value: 3.97e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  161 LPSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFC 240
Cdd:TIGR00446  49 LFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVIN 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  241 FDATKAlkldttdgieggPPFLPEsFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVL 317
Cdd:TIGR00446 129 ADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVL 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  318 VYSTCTITLAENEEQVAWALRTFPCLQLqpqEPQIGGEGMvGAGLTLEQLKQLQRFDPSvvplqnmdtdslgearredmi 397
Cdd:TIGR00446 196 VYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF-GINIGKGEVKGALRVFPQ--------------------- 250

                         250
                  ....*....|....*..
gi 260099664  398 wlaNKDCIGFFIAKFLK 414
Cdd:TIGR00446 251 ---NYDCEGFFVAKLRK 264
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 186-320 2.41e-07

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: 48.97  E-value: 2.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 186 KILDMCAAPGGKTTHTAAlmQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKAlkldttdgieggPPFLPES 265
Cdd:cd02440    1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 260099664 266 FDRIILDAPCSgmgqrpnmactwtlkevtSYQPLQRKLLHVAVQLLKPGGVLVYS 320
Cdd:cd02440   67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
61-151 2.79e-07

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 47.64  E-value: 2.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664    61 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYsDINGKckkgakefdgtkvFLGNGISELSRKDIFNglPDL 140
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKG 64

                           90
                   ....*....|.
gi 260099664   141 KGIGIRMTEPI 151
Cdd:smart00359  65 KGLAVKVRRAV 75
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 41-133 4.86e-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: 40.54  E-value: 4.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  41 LPDVLLIPMTGPRKNIerqqgeVIV--GAQcgNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtk 118
Cdd:COG2016   60 FPTLRGLLKYPPEKPV------VTVdmGAV--KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK------------ 119

                         90
                 ....*....|....*
gi 260099664 119 vFLGNGISELSRKDI 133
Cdd:COG2016  120 -PLAVGRALVDGEEM 133
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 61-133 2.60e-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: 36.31  E-value: 2.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260099664   61 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDiNGKckkgakefdgtkvFLGNGISELSRKDI 133
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 55-136 7.48e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.14  E-value: 7.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  55 NIERQQGEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtkvFLGNGISELSRKDIF 134
Cdd:PRK14560  71 KLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEMV 137


                 ..
gi 260099664 135 NG 136
Cdd:PRK14560 138 EE 139
 
Name Accession Description Interval E-value
RsmB COG0144
16S rRNA C967 or C1407 C5-methylase, RsmB/RsmF family [Translation, ribosomal structure and ...
 144-414 3.19e-66

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: 217.95  E-value: 3.19e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 144 GIRMTEPIYLS--PSFDNvlpSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKV 221
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 222 NKLKQNASLLGLHSIRAFCFDATKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQP 298
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 299 LQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVAWALRTFPCLQLQPQEPQIGGEGMVGAGltleqlkqLQRFDPSVv 378
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--------YLRLLPHR- 426

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 260099664 379 plQNMDtdslgearredmiwlankdciGFFIAKFLK 414
Cdd:COG0144  427 --HGTD---------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
164-414 6.06e-62

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 206.57  E-value: 6.06e-62
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 164 YIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDA 243
Cdd:PRK14902 231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 244 TKAlkldttdgieggPPFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYS 320
Cdd:PRK14902 311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 321 TCTITLAENEEQVAWALRTFPCLQLQPQEPqiggegmvgaGLTLEQLKQLQRFDPSVVPLQNmDTDslgearredmiwla 400
Cdd:PRK14902 379 TCTIEKEENEEVIEAFLEEHPEFELVPLQH----------EKPDELVYEVKDGYLQILPNDY-GTD-------------- 433

                        250
                 ....*....|....
gi 260099664 401 nkdciGFFIAKFLK 414
Cdd:PRK14902 434 -----GFFIAKLRK 442
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 175-352 1.24e-58

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 197.84  E-value: 1.24e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 175 VAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIrafcfdatKALKLDTTDG 254
Cdd:PRK14901 244 VAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSI--------KILAADSRNL 315

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 255 IEGGPPFLpESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEE 331
Cdd:PRK14901 316 LELKPQWR-GYFDRILLDAPCSGLGtlhRHPDARWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYATCTLHPAENEA 394

                        170       180
                 ....*....|....*....|.
gi 260099664 332 QVAWALRTFPCLQLQPQEPQI 352
Cdd:PRK14901 395 QIEQFLARHPDWKLEPPKQKI 415
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 176-413 3.06e-52

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: 173.76  E-value: 3.06e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  176 AHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKalkldtTDGI 255
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------PDQW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  256 EGGppflpESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQ 332
Cdd:pfam01189  75 LGG-----VLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  333 VAWALRTFPCLQLQPqepqIGGEGMVGAGLTLEQLKQlqrfdpsVVPLQNmdtdslgearredmiwlaNKDciGFFIAKF 412
Cdd:pfam01189 150 IEYFLQKHPDVELVP----TPLFEPVGLAIGEQPTLR-------LLPHTH------------------NGD--GFFIAKL 198


                  .
gi 260099664  413 L 413
Cdd:pfam01189 199 R 199
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 62-151 3.03e-50

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: 164.54  E-value: 3.03e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  62 EVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 140
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|.
gi 260099664 141 KGIGIRMTEPI 151
Cdd:cd21150   82 SGIAVEMTEPV 92
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 161-414 3.97e-47

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 162.64  E-value: 3.97e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  161 LPSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFC 240
Cdd:TIGR00446  49 LFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVIN 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  241 FDATKAlkldttdgieggPPFLPEsFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVL 317
Cdd:TIGR00446 129 ADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVL 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  318 VYSTCTITLAENEEQVAWALRTFPCLQLqpqEPQIGGEGMvGAGLTLEQLKQLQRFDPSvvplqnmdtdslgearredmi 397
Cdd:TIGR00446 196 VYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF-GINIGKGEVKGALRVFPQ--------------------- 250

                         250
                  ....*....|....*..
gi 260099664  398 wlaNKDCIGFFIAKFLK 414
Cdd:TIGR00446 251 ---NYDCEGFFVAKLRK 264
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 179-364 2.30e-45

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 162.92  E-value: 2.30e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 179 LDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKalkldttdgiegg 258
Cdd:PRK14904 246 LNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARS------------- 312

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 259 ppFLPE-SFDRIILDAPCSG---MGQRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVA 334
Cdd:PRK14904 313 --FSPEeQPDAILLDAPCTGtgvLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATCSIEPEENELQIE 390

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 260099664 335 WALRTFPCLQLQPQ-----EPQIGGEGMVGAGLTL 364
Cdd:PRK14904 391 AFLQRHPEFSAEPSpgslpEPFHEVAHPKGAILTL 425
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 167-354 5.51e-39

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: 145.01  E-value: 5.51e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  167 LQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQdKGEVIALDKILTKVNKLKQNASLLGLhsirafcfdatkA 246
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQVVALDIHEHRLKRVYENLKRLGL------------T 288

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  247 LKLDTTDGIEGGPPFLPES--FDRIILDAPCSGMG---QRPNMacTWTLKEVTSYQ--PLQRKLLHVAVQLLKPGGVLVY 319
Cdd:TIGR00563 289 IKAETKDGDGRGPSQWAENeqFDRILLDAPCSATGvirRHPDI--KWLRKPRDIAElaELQSEILDAIWPLLKTGGTLVY 366

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 260099664  320 STCTITLAENEEQVAWALRTFPCLQL----QPQEPQIGG 354
Cdd:TIGR00563 367 ATCSVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
176-348 1.67e-36

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 138.40  E-value: 1.67e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 176 AHVLDPQPGEKILDMCAAPGGKTTHTAALmQDKGEVIALDKILTKVNKLKQNASLLGLHSiRAFCFDATkalklDTTDGI 255
Cdd:PRK10901 237 ATLLAPQNGERVLDACAAPGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGDAR-----DPAQWW 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 256 EGGPpflpesFDRIILDAPCSGMG-----------QRPNmactwtlkEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTI 324
Cdd:PRK10901 310 DGQP------FDRILLDAPCSATGvirrhpdikwlRRPE--------DIAALAALQSEILDALWPLLKPGGTLLYATCSI 375

                        170       180
                 ....*....|....*....|....
gi 260099664 325 TLAENEEQVAWALRTFPCLQLQPQ 348
Cdd:PRK10901 376 LPEENEQQIKAFLARHPDAELLDT 399
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 170-341 3.72e-30

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 121.55  E-value: 3.72e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 170 LPstVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATkalkl 249
Cdd:PRK11933 102 LP--VAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVALTHFDGR----- 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 250 dttdgIEGGppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITL 326
Cdd:PRK11933 175 -----VFGA--ALPETFDAILLDAPCSGEGtvrKDPDALKNWSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNR 247

                        170
                 ....*....|....*
gi 260099664 327 AENEEQVAWALRTFP 341
Cdd:PRK11933 248 EENQAVCLWLKETYP 262
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 164-339 3.76e-30

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 120.75  E-value: 3.76e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 164 YIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDA 243
Cdd:PRK14903 218 LATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADA 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 244 TKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYS 320
Cdd:PRK14903 298 ERLTE------------YVQDTFDRILVDAPCTSLGtarNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYS 365

                        170       180
                 ....*....|....*....|
gi 260099664 321 TCTITLAENEEQV-AWALRT 339
Cdd:PRK14903 366 TCTVTKEENTEVVkRFVYEQ 385
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 61-150 6.40e-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: 66.55  E-value: 6.40e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  61 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDiNGKckkgakefdgtkvFLGNGISELSRKDIfngLPDL 140
Cdd:cd07953    1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSE-GGR-------------PLAIGVAEMSSDEM---KEEL 63

                         90
                 ....*....|
gi 260099664 141 KGIGIRMTEP 150
Cdd:cd07953   64 KGIAVRVLHF 73
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 157-318 2.31e-07

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: 49.99  E-value: 2.31e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 157 FDNVLPSYIFLQNLpstvvAHVLDPQPGEKILDMCAAPGgktTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHsI 236
Cdd:COG2226    1 FDRVAARYDGREAL-----LAALGLRPGARVLDLGCGTG---RLALALAERGARVTGVDISPEMLELARERAAEAGLN-V 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 237 RAFCFDATKalkldttdgieggPPFLPESFDRIIldapcsgmgqrpnmaCTWTLKEVTSyqplQRKLLHVAVQLLKPGGV 316
Cdd:COG2226   72 EFVVGDAED-------------LPFPDGSFDLVI---------------SSFVLHHLPD----PERALAEIARVLKPGGR 119


                 ..
gi 260099664 317 LV 318
Cdd:COG2226  120 LV 121
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 186-320 2.41e-07

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: 48.97  E-value: 2.41e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 186 KILDMCAAPGGKTTHTAAlmQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKAlkldttdgieggPPFLPES 265
Cdd:cd02440    1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 260099664 266 FDRIILDAPCSgmgqrpnmactwtlkevtSYQPLQRKLLHVAVQLLKPGGVLVYS 320
Cdd:cd02440   67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
61-151 2.79e-07

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 47.64  E-value: 2.79e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664    61 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYsDINGKckkgakefdgtkvFLGNGISELSRKDIFNglPDL 140
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKG 64

                           90
                   ....*....|.
gi 260099664   141 KGIGIRMTEPI 151
Cdd:smart00359  65 KGLAVKVRRAV 75
Trm5 COG2520
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 183-319 4.23e-05

tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 N-methylase Trm5 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 442010 [Multi-domain]  Cd Length: 333  Bit Score: 45.24  E-value: 4.23e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 183 PGEKILDMCAAPGGKTTHTAALmqDKGEVIALDKILTKVNKLKQNASLLGL-HSIRAFCFDATKAlkldttdgieggPPF 261
Cdd:COG2520  180 PGERVLDMFAGVGPFSIPIAKR--SGAKVVAIDINPDAVEYLKENIRLNKVeDRVTPILGDAREV------------APE 245

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 260099664 262 LPESFDRIILDAPCSGmgqrpnmactwtlkevtsyqplqRKLLHVAVQLLKPGGVLVY 319
Cdd:COG2520  246 LEGKADRIIMNLPHSA-----------------------DEFLDAALRALKPGGVIHY 280
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 182-321 1.56e-04

tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 N-methylase Trm11 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440663 [Multi-domain]  Cd Length: 172  Bit Score: 42.24  E-value: 1.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 182 QPGEKILD-MCaapGGKTT-HTAALMqdKGEVIALDkILTK-VNKLKQNASLLGLHSIRAFCFDATKalkldttdgiegg 258
Cdd:COG1041   25 KEGDTVLDpFC---GTGTIlIEAGLL--GRRVIGSD-IDPKmVEGARENLEHYGYEDADVIRGDARD------------- 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260099664 259 PPFLPESFDRIILDAPcsgMGQRPnmacTWTLKEVTSyqpLQRKLLHVAVQLLKPGGVLVYST 321
Cdd:COG1041   86 LPLADESVDAIVTDPP---YGRSS----KISGEELLE---LYEKALEEAARVLKPGGRVVIVT 138
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 225-338 2.56e-04

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: 42.86  E-value: 2.56e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 225 KQNASLLGL----HSIRAFCFDATKALKLDttdgieggppflPESFDRIILDAPcsgmgqrpnmacTWT-----LKEVts 295
Cdd:COG1092  256 KENAALNGLddrhEFVQADAFDWLRELARE------------GERFDLIILDPP------------AFAkskkdLFDA-- 309

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 260099664 296 yqplQR---KLLHVAVQLLKPGGVLVYSTCT--ITLAENEEQVAWALR 338
Cdd:COG1092  310 ----QRdykDLNRLALKLLAPGGILVTSSCSrhFSLDLFLEILARAAR 353
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 41-133 4.86e-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: 40.54  E-value: 4.86e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  41 LPDVLLIPMTGPRKNIerqqgeVIV--GAQcgNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtk 118
Cdd:COG2016   60 FPTLRGLLKYPPEKPV------VTVdmGAV--KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK------------ 119

                         90
                 ....*....|....*
gi 260099664 119 vFLGNGISELSRKDI 133
Cdd:COG2016  120 -PLAVGRALVDGEEM 133
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 183-321 8.27e-04

2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and metabolism]; 2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase is part of the Pathway/BioSystem: Ubiquinone biosynthesis


Pssm-ID: 441829 [Multi-domain]  Cd Length: 126  Bit Score: 39.23  E-value: 8.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 183 PGEKILDMCAAPGgkttHTAALMQDKG-EVIALDKILTKVNKLKQNASLLGlhsIRAFCFDATKAlkldttdgieggpPF 261
Cdd:COG2227   24 AGGRVLDVGCGTG----RLALALARRGaDVTGVDISPEALEIARERAAELN---VDFVQGDLEDL-------------PL 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 262 LPESFDRIIldapCSgmgqrpnmactwtlkEVTSYQPLQRKLLHVAVQLLKPGGVLVYST 321
Cdd:COG2227   84 EDGSFDLVI----CS---------------EVLEHLPDPAALLRELARLLKPGGLLLLST 124
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 183-318 2.09e-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: 2.09e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  183 PGEKILDMCAAPGGKTthTAALMQDKGEVIALDKILTKVNKLKQNAsllGLHSIRAfcfDATkalKLDTTDGIEggpPFL 262
Cdd:pfam01728  21 PGKTVLDLGAAPGGWS--QVALQRGAGKVVGVDLGPMQLWKPRNDP---GVTFIQG---DIR---DPETLDLLE---ELL 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 260099664  263 PESFDRIILDApcsgmgqRPNMACTWTLKEVTSYQpLQRKLLHVAVQLLKPGGVLV 318
Cdd:pfam01728  87 GRKVDLVLSDG-------SPFISGNKVLDHLRSLD-LVKAALEVALELLRKGGNFV 134
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 61-133 2.60e-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: 36.31  E-value: 2.60e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260099664   61 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDiNGKckkgakefdgtkvFLGNGISELSRKDI 133
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 183-322 3.07e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 38.17  E-value: 3.07e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  183 PGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRafcFDATKALKLDTTdgieggppFL 262
Cdd:pfam13847   3 KGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLGFDNVE---FEQGDIEELPEL--------LE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  263 PESFDRIILDapcsgmgqrpnmactwtlkEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTC 322
Cdd:pfam13847  72 DDKFDVVISN-------------------CVLNHIPDPDKVLQEILRVLKPGGRLIISDP 112
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 158-320 4.33e-03

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


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 38.36  E-value: 4.33e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 158 DNVLPSYIFLqnlpstvVAHVLDPQPGEKILDMCAAPGgktTHTAALMQ-DKGEVIALDKILTKVNKLKQNASLLGLHSI 236
Cdd:COG0500    8 DELLPGLAAL-------LALLERLPKGGRVLDLGCGTG---RNLLALAArFGGRVIGIDLSPEAIALARARAAKAGLGNV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664 237 RAFCFDATKALKLDttdgieggppflPESFDRIILdapcsgmgqrpNMACTWTLKEVtsyqplQRKLLHVAVQLLKPGGV 316
Cdd:COG0500   78 EFLVADLAELDPLP------------AESFDLVVA-----------FGVLHHLPPEE------REALLRELARALKPGGV 128


                 ....
gi 260099664 317 LVYS 320
Cdd:COG0500  129 LLLS 132
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 187-315 7.28e-03

Methyltransferase domain; This family appears to be a methyltransferase domain.


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 35.62  E-value: 7.28e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  187 ILDMCAAPGgktTHTAALMQDKG-EVIALDKILTKVNKLKQNASLLGLHsIRAFCFDATKalkldttdgieggPPFLPES 265
Cdd:pfam13649   1 VLDLGCGTG---RLTLALARRGGaRVTGVDLSPEMLERARERAAEAGLN-VEFVQGDAED-------------LPFPDGS 63

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|
gi 260099664  266 FDRIIldapcsgmgqrpnmaCTWTLKEVTsyQPLQRKLLHVAVQLLKPGG 315
Cdd:pfam13649  64 FDLVV---------------SSGVLHHLP--DPDLEAALREIARVLKPGG 96
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 55-136 7.48e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.14  E-value: 7.48e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099664  55 NIERQQGEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtkvFLGNGISELSRKDIF 134
Cdd:PRK14560  71 KLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEMV 137


                 ..
gi 260099664 135 NG 136
Cdd:PRK14560 138 EE 139
 
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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