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Conserved domains on  [gi|260099660|ref|NP_001159413|]
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tRNA (cytosine(72)-C(5))-methyltransferase NSUN6 isoform a [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 ...
 195-465 1.39e-65

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: 217.57  E-value: 1.39e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 195 GIRMTEPIYLS--PSFDNvlpSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKV 272
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 273 NKLKQNASLLGLHSIRAFCFDATKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQP 349
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 350 LQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVAWALRTFPCLQLQPQEPQIGGEGMVGAGltleqlkqLQRFDPSVv 429
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--------YLRLLPHR- 426

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 260099660 430 plQNMDtdslgearredmiwlankdciGFFIAKFLK 465
Cdd:COG0144  427 --HGTD---------------------GFFIARLRK 439
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 113-202 2.14e-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: 166.47  E-value: 2.14e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 113 EVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 191
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|.
gi 260099660 192 KGIGIRMTEPI 202
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 ...
 195-465 1.39e-65

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: 217.57  E-value: 1.39e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 195 GIRMTEPIYLS--PSFDNvlpSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKV 272
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 273 NKLKQNASLLGLHSIRAFCFDATKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQP 349
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 350 LQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVAWALRTFPCLQLQPQEPQIGGEGMVGAGltleqlkqLQRFDPSVv 429
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--------YLRLLPHR- 426

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 260099660 430 plQNMDtdslgearredmiwlankdciGFFIAKFLK 465
Cdd:COG0144  427 --HGTD---------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
215-465 3.57e-61

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 206.18  E-value: 3.57e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 215 YIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDA 294
Cdd:PRK14902 231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 295 TKAlkldttdgieggPPFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYS 371
Cdd:PRK14902 311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 372 TCTITLAENEEQVAWALRTFPCLQLQPQEPqiggegmvgaGLTLEQLKQLQRFDPSVVPLQNmDTDslgearredmiwla 451
Cdd:PRK14902 379 TCTIEKEENEEVIEAFLEEHPEFELVPLQH----------EKPDELVYEVKDGYLQILPNDY-GTD-------------- 433

                        250
                 ....*....|....
gi 260099660 452 nkdciGFFIAKFLK 465
Cdd:PRK14902 434 -----GFFIAKLRK 442
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 227-464 9.67e-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: 9.67e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  227 AHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKalkldtTDGI 306
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------PDQW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  307 EGGppflpESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQ 383
Cdd:pfam01189  75 LGG-----VLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  384 VAWALRTFPCLQLQPqepqIGGEGMVGAGLTLEQLKQlqrfdpsVVPLQNmdtdslgearredmiwlaNKDciGFFIAKF 463
Cdd:pfam01189 150 IEYFLQKHPDVELVP----TPLFEPVGLAIGEQPTLR-------LLPHTH------------------NGD--GFFIAKL 198


                  .
gi 260099660  464 L 464
Cdd:pfam01189 199 R 199
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 113-202 2.14e-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: 166.47  E-value: 2.14e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 113 EVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 191
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|.
gi 260099660 192 KGIGIRMTEPI 202
Cdd:cd21150   82 SGIAVEMTEPV 92
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 212-465 2.61e-46

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 161.48  E-value: 2.61e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  212 LPSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFC 291
Cdd:TIGR00446  49 LFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVIN 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  292 FDATKAlkldttdgieggPPFLPEsFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVL 368
Cdd:TIGR00446 129 ADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVL 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  369 VYSTCTITLAENEEQVAWALRTFPCLQLqpqEPQIGGEGMvGAGLTLEQLKQLQRFDPSvvplqnmdtdslgearredmi 448
Cdd:TIGR00446 196 VYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF-GINIGKGEVKGALRVFPQ--------------------- 250

                         250
                  ....*....|....*..
gi 260099660  449 wlaNKDCIGFFIAKFLK 465
Cdd:TIGR00446 251 ---NYDCEGFFVAKLRK 264
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 237-371 1.70e-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: 49.35  E-value: 1.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 237 KILDMCAAPGGKTTHTAAlmQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKAlkldttdgieggPPFLPES 316
Cdd:cd02440    1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 260099660 317 FDRIILDAPCSgmgqrpnmactwtlkevtSYQPLQRKLLHVAVQLLKPGGVLVYS 371
Cdd:cd02440   67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
112-202 2.23e-07

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 48.02  E-value: 2.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660   112 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYsDINGKckkgakefdgtkvFLGNGISELSRKDIFNglPDL 191
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKG 64

                           90
                   ....*....|.
gi 260099660   192 KGIGIRMTEPI 202
Cdd:smart00359  65 KGLAVKVRRAV 75
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 92-184 5.42e-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: 5.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  92 LPDVLLIPMTGPRKNIerqqgeVIV--GAQcgNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtk 169
Cdd:COG2016   60 FPTLRGLLKYPPEKPV------VTVdmGAV--KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK------------ 119

                         90
                 ....*....|....*
gi 260099660 170 vFLGNGISELSRKDI 184
Cdd:COG2016  120 -PLAVGRALVDGEEM 133
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 112-184 2.27e-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: 36.69  E-value: 2.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260099660  112 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDiNGKckkgakefdgtkvFLGNGISELSRKDI 184
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 106-187 8.35e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.14  E-value: 8.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 106 NIERQQGEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtkvFLGNGISELSRKDIF 185
Cdd:PRK14560  71 KLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEMV 137


                 ..
gi 260099660 186 NG 187
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 ...
 195-465 1.39e-65

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: 217.57  E-value: 1.39e-65
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 195 GIRMTEPIYLS--PSFDNvlpSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKV 272
Cdd:COG0144  211 GLRLEGPGPVTalPGFRE---GLFSVQDEASQLVALLLDPKPGERVLDLCAAPGGKTLHLAELMGNKGRVVAVDISEHRL 287

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 273 NKLKQNASLLGLHSIRAFCFDATKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQP 349
Cdd:COG0144  288 KRLRENLARLGLSNVEVVVADARELLE------------WLPGKFDRVLLDAPCSGTGtlrRHPDIKWRRTPEDIAELAA 355

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 350 LQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVAWALRTFPCLQLQPQEPQIGGEGMVGAGltleqlkqLQRFDPSVv 429
Cdd:COG0144  356 LQRELLDAAARLLKPGGRLVYSTCSLLPEENEEVVEAFLARHPDFELVPLAELLPGLALTDGG--------YLRLLPHR- 426

                        250       260       270
                 ....*....|....*....|....*....|....*.
gi 260099660 430 plQNMDtdslgearredmiwlankdciGFFIAKFLK 465
Cdd:COG0144  427 --HGTD---------------------GFFIARLRK 439
PRK14902 PRK14902
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
215-465 3.57e-61

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


Pssm-ID: 237857 [Multi-domain]  Cd Length: 444  Bit Score: 206.18  E-value: 3.57e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 215 YIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDA 294
Cdd:PRK14902 231 LITIQDESSMLVAPALDPKGGDTVLDACAAPGGKTTHIAELLKNTGKVVALDIHEHKLKLIEENAKRLGLTNIETKALDA 310

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 295 TKAlkldttdgieggPPFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYS 371
Cdd:PRK14902 311 RKV------------HEKFAEKFDKILVDAPCSGLGvirRKPDIKYNKTKEDIESLQEIQLEILESVAQYLKKGGILVYS 378

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 372 TCTITLAENEEQVAWALRTFPCLQLQPQEPqiggegmvgaGLTLEQLKQLQRFDPSVVPLQNmDTDslgearredmiwla 451
Cdd:PRK14902 379 TCTIEKEENEEVIEAFLEEHPEFELVPLQH----------EKPDELVYEVKDGYLQILPNDY-GTD-------------- 433

                        250
                 ....*....|....
gi 260099660 452 nkdciGFFIAKFLK 465
Cdd:PRK14902 434 -----GFFIAKLRK 442
PRK14901 PRK14901
16S rRNA methyltransferase B; Provisional
 226-403 3.69e-58

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237856 [Multi-domain]  Cd Length: 434  Bit Score: 197.84  E-value: 3.69e-58
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 226 VAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIrafcfdatKALKLDTTDG 305
Cdd:PRK14901 244 VAPLLDPQPGEVILDACAAPGGKTTHIAELMGDQGEIWAVDRSASRLKKLQENAQRLGLKSI--------KILAADSRNL 315

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 306 IEGGPPFLpESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEE 382
Cdd:PRK14901 316 LELKPQWR-GYFDRILLDAPCSGLGtlhRHPDARWRQTPEKIQELAPLQAELLESLAPLLKPGGTLVYATCTLHPAENEA 394

                        170       180
                 ....*....|....*....|.
gi 260099660 383 QVAWALRTFPCLQLQPQEPQI 403
Cdd:PRK14901 395 QIEQFLARHPDWKLEPPKQKI 415
Methyltr_RsmB-F pfam01189
16S rRNA methyltransferase RsmB/F; This is the catalytic core of this SAM-dependent 16S ...
 227-464 9.67e-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: 9.67e-52
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  227 AHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKalkldtTDGI 306
Cdd:pfam01189   1 AILLAPQEGETILDMCAAPGGKTTHIAELMKNQGTVVAVDINKHRLKRVAENIHRLGVTNTIILNGDGRQ------PDQW 74

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  307 EGGppflpESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQ 383
Cdd:pfam01189  75 LGG-----VLFDRILLDAPCSGTGvirRHPDVKWLRQEADIAQLAQLQKELLSAAIDLLKPGGVLVYSTCSVLPEENEAV 149

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  384 VAWALRTFPCLQLQPqepqIGGEGMVGAGLTLEQLKQlqrfdpsVVPLQNmdtdslgearredmiwlaNKDciGFFIAKF 463
Cdd:pfam01189 150 IEYFLQKHPDVELVP----TPLFEPVGLAIGEQPTLR-------LLPHTH------------------NGD--GFFIAKL 198


                  .
gi 260099660  464 L 464
Cdd:pfam01189 199 R 199
PUA_NSun6-like cd21150
PUA RNA-binding domain of the SAM-dependent methyltransferase NSun6 and similar proteins; The ...
 113-202 2.14e-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: 166.47  E-value: 2.14e-50
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 113 EVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKCKKGA-KEFDGTKVFLGNGISELSRKDIFNGLPDL 191
Cdd:cd21150    2 EVIVDRKCGEAVLRGAHVFAPGVLGAPPGLKKGDKVSVYADLEGKCKRGLtKPFEGRKVFVGNGIALMSRKDLFRGNNKP 81

                         90
                 ....*....|.
gi 260099660 192 KGIGIRMTEPI 202
Cdd:cd21150   82 SGIAVEMTEPV 92
nop2p TIGR00446
NOL1/NOP2/sun family putative RNA methylase; [Protein synthesis, tRNA and rRNA base ...
 212-465 2.61e-46

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


Pssm-ID: 188051 [Multi-domain]  Cd Length: 264  Bit Score: 161.48  E-value: 2.61e-46
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  212 LPSYIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFC 291
Cdd:TIGR00446  49 LFGYYYPQEASSMIPPIALEPREDERVLDMAAAPGGKTTQISQLMKNKGCIVANEISKSRTKALISNINRMGVLNTIVIN 128

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  292 FDATKAlkldttdgieggPPFLPEsFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVL 368
Cdd:TIGR00446 129 ADGRKF------------GAYLLK-FDAILLDAPCSGEGvirKDPSRKRNWSEEDIKYCSLLQKELIDAAIDALKPGGVL 195

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  369 VYSTCTITLAENEEQVAWALRTFPCLQLqpqEPQIGGEGMvGAGLTLEQLKQLQRFDPSvvplqnmdtdslgearredmi 448
Cdd:TIGR00446 196 VYSTCSLEVEENEEVIDYILRKRPDVVE---EIIKGDEFF-GINIGKGEVKGALRVFPQ--------------------- 250

                         250
                  ....*....|....*..
gi 260099660  449 wlaNKDCIGFFIAKFLK 465
Cdd:TIGR00446 251 ---NYDCEGFFVAKLRK 264
PRK14904 PRK14904
16S rRNA methyltransferase B; Provisional
 230-415 6.80e-45

16S rRNA methyltransferase B; Provisional


Pssm-ID: 237858 [Multi-domain]  Cd Length: 445  Bit Score: 162.92  E-value: 6.80e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 230 LDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKalkldttdgiegg 309
Cdd:PRK14904 246 LNPQPGSTVLDLCAAPGGKSTFMAELMQNRGQITAVDRYPQKLEKIRSHASALGITIIETIEGDARS------------- 312

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 310 ppFLPE-SFDRIILDAPCSG---MGQRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITLAENEEQVA 385
Cdd:PRK14904 313 --FSPEeQPDAILLDAPCTGtgvLGRRAELRWKLTPEKLAELVGLQAELLDHAASLLKPGGVLVYATCSIEPEENELQIE 390

                        170       180       190
                 ....*....|....*....|....*....|....*
gi 260099660 386 WALRTFPCLQLQPQ-----EPQIGGEGMVGAGLTL 415
Cdd:PRK14904 391 AFLQRHPEFSAEPSpgslpEPFHEVAHPKGAILTL 425
rsmB TIGR00563
16S rRNA (cytosine(967)-C(5))-methyltransferase; This protein is also known as sun protein. ...
 218-405 2.01e-38

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: 144.63  E-value: 2.01e-38
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  218 LQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQdKGEVIALDKILTKVNKLKQNASLLGLhsirafcfdatkA 297
Cdd:TIGR00563 222 VQDASAQWVATWLAPQNEETILDACAAPGGKTTHILELAP-QAQVVALDIHEHRLKRVYENLKRLGL------------T 288

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  298 LKLDTTDGIEGGPPFLPES--FDRIILDAPCSGMG---QRPNMacTWTLKEVTSYQ--PLQRKLLHVAVQLLKPGGVLVY 370
Cdd:TIGR00563 289 IKAETKDGDGRGPSQWAENeqFDRILLDAPCSATGvirRHPDI--KWLRKPRDIAElaELQSEILDAIWPLLKTGGTLVY 366

                         170       180       190
                  ....*....|....*....|....*....|....*....
gi 260099660  371 STCTITLAENEEQVAWALRTFPCLQL----QPQEPQIGG 405
Cdd:TIGR00563 367 ATCSVLPEENSEQIKAFLQEHPDFPFektgTPEQVRDGG 405
PRK10901 PRK10901
16S rRNA (cytosine(967)-C(5))-methyltransferase RsmB;
227-399 4.06e-36

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


Pssm-ID: 236790 [Multi-domain]  Cd Length: 427  Bit Score: 138.40  E-value: 4.06e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 227 AHVLDPQPGEKILDMCAAPGGKTTHTAALmQDKGEVIALDKILTKVNKLKQNASLLGLHSiRAFCFDATkalklDTTDGI 306
Cdd:PRK10901 237 ATLLAPQNGERVLDACAAPGGKTAHILEL-APQAQVVALDIDAQRLERVRENLQRLGLKA-TVIVGDAR-----DPAQWW 309

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 307 EGGPpflpesFDRIILDAPCSGMG-----------QRPNmactwtlkEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTI 375
Cdd:PRK10901 310 DGQP------FDRILLDAPCSATGvirrhpdikwlRRPE--------DIAALAALQSEILDALWPLLKPGGTLLYATCSI 375

                        170       180
                 ....*....|....*....|....
gi 260099660 376 TLAENEEQVAWALRTFPCLQLQPQ 399
Cdd:PRK10901 376 LPEENEQQIKAFLARHPDAELLDT 399
yebU PRK11933
rRNA (cytosine-C(5)-)-methyltransferase RsmF; Reviewed
 221-392 7.68e-30

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


Pssm-ID: 183387 [Multi-domain]  Cd Length: 470  Bit Score: 121.55  E-value: 7.68e-30
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 221 LPstVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATkalkl 300
Cdd:PRK11933 102 LP--VAALFADDNAPQRVLDMAAAPGSKTTQIAALMNNQGAIVANEYSASRVKVLHANISRCGVSNVALTHFDGR----- 174

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 301 dttdgIEGGppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTCTITL 377
Cdd:PRK11933 175 -----VFGA--ALPETFDAILLDAPCSGEGtvrKDPDALKNWSPESNLEIAATQRELIESAFHALKPGGTLVYSTCTLNR 247

                        170
                 ....*....|....*
gi 260099660 378 AENEEQVAWALRTFP 392
Cdd:PRK11933 248 EENQAVCLWLKETYP 262
PRK14903 PRK14903
16S rRNA methyltransferase B; Provisional
 215-390 2.54e-29

16S rRNA methyltransferase B; Provisional


Pssm-ID: 184896 [Multi-domain]  Cd Length: 431  Bit Score: 119.21  E-value: 2.54e-29
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 215 YIFLQNLPSTVVAHVLDPQPGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDA 294
Cdd:PRK14903 218 LATVQGESSQIVPLLMELEPGLRVLDTCAAPGGKTTAIAELMKDQGKILAVDISREKIQLVEKHAKRLKLSSIEIKIADA 297

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 295 TKALKldttdgieggppFLPESFDRIILDAPCSGMG---QRPNMACTWTLKEVTSYQPLQRKLLHVAVQLLKPGGVLVYS 371
Cdd:PRK14903 298 ERLTE------------YVQDTFDRILVDAPCTSLGtarNHPEVLRRVNKEDFKKLSEIQLRIVSQAWKLLEKGGILLYS 365

                        170       180
                 ....*....|....*....|
gi 260099660 372 TCTITLAENEEQV-AWALRT 390
Cdd:PRK14903 366 TCTVTKEENTEVVkRFVYEQ 385
PUA cd07953
PUA RNA binding domain; The PUA (PseudoUridine synthase and Archaeosine transglycosylase) ...
 112-201 5.42e-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: 66.94  E-value: 5.42e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 112 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDiNGKckkgakefdgtkvFLGNGISELSRKDIfngLPDL 191
Cdd:cd07953    1 PVVVVDKGAEKAVLNGADLMAPGVVSADGDFKRGDLVRIVSE-GGR-------------PLAIGVAEMSSDEM---KEEL 63

                         90
                 ....*....|
gi 260099660 192 KGIGIRMTEP 201
Cdd:cd07953   64 KGIAVRVLHF 73
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 237-371 1.70e-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: 49.35  E-value: 1.70e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 237 KILDMCAAPGGKTTHTAAlmQDKGEVIALDKILTKVNKLKQNASLLGLHSIRAFCFDATKAlkldttdgieggPPFLPES 316
Cdd:cd02440    1 RVLDLGCGTGALALALAS--GPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEEL------------PPEADES 66

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 260099660 317 FDRIILDAPCSgmgqrpnmactwtlkevtSYQPLQRKLLHVAVQLLKPGGVLVYS 371
Cdd:cd02440   67 FDVIISDPPLH------------------HLVEDLARFLEEARRLLKPGGVLVLT 103
PUA smart00359
Putative RNA-binding Domain in PseudoUridine synthase and Archaeosine transglycosylase;
112-202 2.23e-07

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


Pssm-ID: 214635 [Multi-domain]  Cd Length: 76  Bit Score: 48.02  E-value: 2.23e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660   112 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYsDINGKckkgakefdgtkvFLGNGISELSRKDIFNglPDL 191
Cdd:smart00359   1 GKVVVDDGAEKAILNGASLLAPGVVRVDGDIKEGDVVVIV-DEKGE-------------PLGIGLANMSSEEIAR--IKG 64

                           90
                   ....*....|.
gi 260099660   192 KGIGIRMTEPI 202
Cdd:smart00359  65 KGLAVKVRRAV 75
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 208-369 2.65e-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: 2.65e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 208 FDNVLPSYIFLQNLpstvvAHVLDPQPGEKILDMCAAPGgktTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHsI 287
Cdd:COG2226    1 FDRVAARYDGREAL-----LAALGLRPGARVLDLGCGTG---RLALALAERGARVTGVDISPEMLELARERAAEAGLN-V 71

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 288 RAFCFDATKalkldttdgieggPPFLPESFDRIIldapcsgmgqrpnmaCTWTLKEVTSyqplQRKLLHVAVQLLKPGGV 367
Cdd:COG2226   72 EFVVGDAED-------------LPFPDGSFDLVI---------------SSFVLHHLPD----PERALAEIARVLKPGGR 119


                 ..
gi 260099660 368 LV 369
Cdd:COG2226  120 LV 121
Trm5 COG2520
tRNA G37 N-methylase Trm5 [Translation, ribosomal structure and biogenesis]; tRNA G37 ...
 234-370 5.03e-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: 5.03e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 234 PGEKILDMCAAPGGKTTHTAALmqDKGEVIALDKILTKVNKLKQNASLLGL-HSIRAFCFDATKAlkldttdgieggPPF 312
Cdd:COG2520  180 PGERVLDMFAGVGPFSIPIAKR--SGAKVVAIDINPDAVEYLKENIRLNKVeDRVTPILGDAREV------------APE 245

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 260099660 313 LPESFDRIILDAPCSGmgqrpnmactwtlkevtsyqplqRKLLHVAVQLLKPGGVLVY 370
Cdd:COG2520  246 LEGKADRIIMNLPHSA-----------------------DEFLDAALRALKPGGVIHY 280
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 233-372 1.79e-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: 1.79e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 233 QPGEKILD-MCaapGGKTT-HTAALMqdKGEVIALDkILTK-VNKLKQNASLLGLHSIRAFCFDATKalkldttdgiegg 309
Cdd:COG1041   25 KEGDTVLDpFC---GTGTIlIEAGLL--GRRVIGSD-IDPKmVEGARENLEHYGYEDADVIRGDARD------------- 85

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260099660 310 PPFLPESFDRIILDAPcsgMGQRPnmacTWTLKEVTSyqpLQRKLLHVAVQLLKPGGVLVYST 372
Cdd:COG1041   86 LPLADESVDAIVTDPP---YGRSS----KISGEELLE---LYEKALEEAARVLKPGGRVVIVT 138
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 276-389 3.04e-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: 3.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 276 KQNASLLGL----HSIRAFCFDATKALKLDttdgieggppflPESFDRIILDAPcsgmgqrpnmacTWT-----LKEVts 346
Cdd:COG1092  256 KENAALNGLddrhEFVQADAFDWLRELARE------------GERFDLIILDPP------------AFAkskkdLFDA-- 309

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*...
gi 260099660 347 yqplQR---KLLHVAVQLLKPGGVLVYSTCT--ITLAENEEQVAWALR 389
Cdd:COG1092  310 ----QRdykDLNRLALKLLAPGGILVTSSCSrhFSLDLFLEILARAAR 353
Tma20 COG2016
Predicted ribosome-associated RNA-binding protein Tma20, contains PUA domain [Translation, ...
 92-184 5.42e-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: 5.42e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  92 LPDVLLIPMTGPRKNIerqqgeVIV--GAQcgNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtk 169
Cdd:COG2016   60 FPTLRGLLKYPPEKPV------VTVdmGAV--KFVSNGADVMRPGIVEADGEIKEGDIVVIVEEKHGK------------ 119

                         90
                 ....*....|....*
gi 260099660 170 vFLGNGISELSRKDI 184
Cdd:COG2016  120 -PLAVGRALVDGEEM 133
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 234-372 9.43e-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: 9.43e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 234 PGEKILDMCAAPGgkttHTAALMQDKG-EVIALDKILTKVNKLKQNASLLGlhsIRAFCFDATKAlkldttdgieggpPF 312
Cdd:COG2227   24 AGGRVLDVGCGTG----RLALALARRGaDVTGVDISPEALEIARERAAELN---VDFVQGDLEDL-------------PL 83

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 313 LPESFDRIIldapCSgmgqrpnmactwtlkEVTSYQPLQRKLLHVAVQLLKPGGVLVYST 372
Cdd:COG2227   84 EDGSFDLVI----CS---------------EVLEHLPDPAALLRELARLLKPGGLLLLST 124
FtsJ pfam01728
FtsJ-like methyltransferase; This family consists of FtsJ from various bacterial and archaeal ...
 234-369 2.08e-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: 39.11  E-value: 2.08e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  234 PGEKILDMCAAPGGKTthTAALMQDKGEVIALDKILTKVNKLKQNAsllGLHSIRAfcfDATkalKLDTTDGIEggpPFL 313
Cdd:pfam01728  21 PGKTVLDLGAAPGGWS--QVALQRGAGKVVGVDLGPMQLWKPRNDP---GVTFIQG---DIR---DPETLDLLE---ELL 86

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 260099660  314 PESFDRIILDApcsgmgqRPNMACTWTLKEVTSYQpLQRKLLHVAVQLLKPGGVLV 369
Cdd:pfam01728  87 GRKVDLVLSDG-------SPFISGNKVLDHLRSLD-LVKAALEVALELLRKGGNFV 134
PUA pfam01472
PUA domain; The PUA domain named after Pseudouridine synthase and Archaeosine transglycosylase, ...
 112-184 2.27e-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: 36.69  E-value: 2.27e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 260099660  112 GEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDiNGKckkgakefdgtkvFLGNGISELSRKDI 184
Cdd:pfam01472   1 GRVVVDDGAVKAILNGASLLAPGVVRVDGDFRKGDEVVVVTE-KGE-------------LVAVGLANYSSEEL 59
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 234-373 3.14e-03

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 38.17  E-value: 3.14e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  234 PGEKILDMCAAPGGKTTHTAALMQDKGEVIALDKILTKVNKLKQNASLLGLHSIRafcFDATKALKLDTTdgieggppFL 313
Cdd:pfam13847   3 KGMRVLDLGCGTGHLSFELAEELGPNAEVVGIDISEEAIEKARENAQKLGFDNVE---FEQGDIEELPEL--------LE 71

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660  314 PESFDRIILDapcsgmgqrpnmactwtlkEVTSYQPLQRKLLHVAVQLLKPGGVLVYSTC 373
Cdd:pfam13847  72 DDKFDVVISN-------------------CVLNHIPDPDKVLQEILRVLKPGGRLIISDP 112
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 209-371 5.01e-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: 5.01e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 209 DNVLPSYIFLqnlpstvVAHVLDPQPGEKILDMCAAPGgktTHTAALMQ-DKGEVIALDKILTKVNKLKQNASLLGLHSI 287
Cdd:COG0500    8 DELLPGLAAL-------LALLERLPKGGRVLDLGCGTG---RNLLALAArFGGRVIGIDLSPEAIALARARAAKAGLGNV 77

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 288 RAFCFDATKALKLDttdgieggppflPESFDRIILdapcsgmgqrpNMACTWTLKEVtsyqplQRKLLHVAVQLLKPGGV 367
Cdd:COG0500   78 EFLVADLAELDPLP------------AESFDLVVA-----------FGVLHHLPPEE------REALLRELARALKPGGV 128


                 ....
gi 260099660 368 LVYS 371
Cdd:COG0500  129 LLLS 132
PRK14560 PRK14560
putative RNA-binding protein; Provisional
 106-187 8.35e-03

putative RNA-binding protein; Provisional


Pssm-ID: 237757 [Multi-domain]  Cd Length: 160  Bit Score: 37.14  E-value: 8.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 260099660 106 NIERQQGEVIVGAQCGNAVLRGAHVYVPGIVSASKFMKAGDVISVYSDINGKckkgakefdgtkvFLGNGISELSRKDIF 185
Cdd:PRK14560  71 KLKPEKRRVVVDAGAVKFVSNGADVMAPGIVEADEDIKEGDIVFVVEETHGK-------------PLAVGRALMDGDEMV 137


                 ..
gi 260099660 186 NG 187
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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