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Conserved domains on  [gi|2743938658|ref|WP_349675202|]
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TrmH family RNA methyltransferase [Isoptericola variabilis]

Protein Classification

RNA methyltransferase( domain architecture ID 1000317)

SpoU family RNA methyltransferase catalyzes the methylation of rRNA or tRNA at specific sites in a S-adenosyl-L-methionine (SAM)-dependent manner

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
SPOUT_MTase super family cl38912
SPOUT superfamily of SAM-dependent RNA methyltransferases; The SPOUT (SpoU-TrmD) ...
 83-220 2.58e-54

SPOUT superfamily of SAM-dependent RNA methyltransferases; The SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, also known as class IV methyltransferase family, is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot. Members of the SPOUT superfamily that have been characterized functionally are involved in post-transcriptional RNA modification by catalyzing methylation of the 2-OH group of ribose, the N-1 atom of guanosine 37 in tRNA, or the N-3 atom of uridine 1498 in 16S rRNA.


The actual alignment was detected with superfamily member cd18096:

Pssm-ID: 476814  Cd Length: 140  Bit Score: 170.86  E-value: 2.58e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  83 FEVAVENLDHDFNIGSIVRTANAMGARRVHVVGRKRWNRRGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVGVDNVEGS 162
Cdd:cd18096     1 LYLVLHNVAKRHNIGTIVRSANAFGVKEVHLVGRRKFNPFGAMGTDRHVKFRHFDTLAEAKEYLKERGIRLVGVEIVPGA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2743938658 163 IALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGS-TRSMNVGHAAAIVMWA 220
Cdd:cd18096    81 EPIETHPFPGDTAFVLGNEGTGLSDEQLAICDGFVYIPQYGSgTASLNVSVAASIVLHH 139
 
Name Accession Description Interval E-value
SpoU-like cd18096
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 83-220 2.58e-54

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349969  Cd Length: 140  Bit Score: 170.86  E-value: 2.58e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  83 FEVAVENLDHDFNIGSIVRTANAMGARRVHVVGRKRWNRRGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVGVDNVEGS 162
Cdd:cd18096     1 LYLVLHNVAKRHNIGTIVRSANAFGVKEVHLVGRRKFNPFGAMGTDRHVKFRHFDTLAEAKEYLKERGIRLVGVEIVPGA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2743938658 163 IALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGS-TRSMNVGHAAAIVMWA 220
Cdd:cd18096    81 EPIETHPFPGDTAFVLGNEGTGLSDEQLAICDGFVYIPQYGSgTASLNVSVAASIVLHH 139
SpoU_methylase pfam00588
SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
 82-219 5.55e-32

SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.


Pssm-ID: 425768  Cd Length: 142  Bit Score: 113.78  E-value: 5.55e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  82 PFEVAVENLDHDFNIGSIVRTANAMGARRVHVVGRKRWN------RRGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVG 155
Cdd:pfam00588   1 PLVVVLDNIQDPGNLGAIIRTAAAFGADGLILVEPRSADpynpkaIRASAGALFHLPLVVVDNLEEALKDLKEAGYAVVA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2743938658 156 VDNveGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:pfam00588  81 TSL--GGKSLYEIDFPKKVALVFGNEGTGLSNEVLELCDRLVRIPMSGDVESLNVAVAAAIALY 142
SpoU COG0566
tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA ...
 62-220 4.69e-21

tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA G18 (ribose-2'-O)-methylase SpoU is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440332 [Multi-domain]  Cd Length: 265  Bit Score: 88.33  E-value: 4.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  62 DRYRYWRMDAIRADIAARslPFEVAVENL-DHdFNIGSIVRTANAMGARRVhVVGRKR---WNRR------GAMVtdrYL 131
Cdd:COG0566    97 RPPEYADLEDLLAEAGEP--PLLLVLDGVqDP-GNLGAILRSAAAFGVDGV-ILPKRRadpYNPKvvrasaGALF---HV 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 132 PVDHRPEVGELVDHCAREGLTLVGVDnVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVG 211
Cdd:COG0566   170 PVARVTNLADALEELKEAGFWVVGTD-LDGEASLYEVDLPGPVALVLGNEGKGLSRLVLEACDELVRIPMAGGVESLNVA 248


                  ....*....
gi 2743938658 212 HAAAIVMWA 220
Cdd:COG0566   249 VAAAILLYE 257
rRNA_methyl_3 TIGR00186
rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases ...
 64-218 2.35e-10

rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129290 [Multi-domain]  Cd Length: 237  Bit Score: 58.51  E-value: 2.35e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  64 YRYWRMDAIRADIAARSLPFEVAVENLDHDFNIGSIVRTANAMGARRVhVVGRKRWN------RRGAMVTDRYLPVDHRP 137
Cdd:TIGR00186  72 ILYKDLNDLYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGV-ILPKRRSAplnstvVKTSSGAVEYVPLARVT 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 138 EVGELVDHCAREGLTLVGVDnVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIV 217
Cdd:TIGR00186 151 NLSRTITKLKESGFWTVGTD-LDAQDTLYQVKLTKPLALVVGNEGEGVSRLIKENCDFLIKIPMAGKVDSLNVSVAAGIL 229


                  .
gi 2743938658 218 M 218
Cdd:TIGR00186 230 L 230
PRK11081 PRK11081
tRNA guanosine-2'-O-methyltransferase; Provisional
 65-219 2.04e-06

tRNA guanosine-2'-O-methyltransferase; Provisional


Pssm-ID: 236837 [Multi-domain]  Cd Length: 229  Bit Score: 46.91  E-value: 2.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  65 RYWRmdaIRADIAARSLPFEVAVENLDHDFNIGSIVRTANAMGARRVHVV--GRKRWNRRG-AMVTDRYLPVDHRPEVGE 141
Cdd:PRK11081    5 RYAR---ICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVwpGSRMRTMGStAAGSNSWVQVKTHRTIGD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2743938658 142 LVDHCAREGLTLVGVDNVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:PRK11081   82 AVAHLKGQGMQILATHLSDTAVDFREIDYTRPTCILMGQEKTGISQEALALADQDIIIPMIGMVQSLNVSVASALILY 159
 
Name Accession Description Interval E-value
SpoU-like cd18096
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 83-220 2.58e-54

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349969  Cd Length: 140  Bit Score: 170.86  E-value: 2.58e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  83 FEVAVENLDHDFNIGSIVRTANAMGARRVHVVGRKRWNRRGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVGVDNVEGS 162
Cdd:cd18096     1 LYLVLHNVAKRHNIGTIVRSANAFGVKEVHLVGRRKFNPFGAMGTDRHVKFRHFDTLAEAKEYLKERGIRLVGVEIVPGA 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2743938658 163 IALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGS-TRSMNVGHAAAIVMWA 220
Cdd:cd18096    81 EPIETHPFPGDTAFVLGNEGTGLSDEQLAICDGFVYIPQYGSgTASLNVSVAASIVLHH 139
SpoU_methylase pfam00588
SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.
 82-219 5.55e-32

SpoU rRNA Methylase family; This family of proteins probably use S-AdoMet.


Pssm-ID: 425768  Cd Length: 142  Bit Score: 113.78  E-value: 5.55e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  82 PFEVAVENLDHDFNIGSIVRTANAMGARRVHVVGRKRWN------RRGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVG 155
Cdd:pfam00588   1 PLVVVLDNIQDPGNLGAIIRTAAAFGADGLILVEPRSADpynpkaIRASAGALFHLPLVVVDNLEEALKDLKEAGYAVVA 80

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2743938658 156 VDNveGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:pfam00588  81 TSL--GGKSLYEIDFPKKVALVFGNEGTGLSNEVLELCDRLVRIPMSGDVESLNVAVAAAIALY 142
SpoU-like cd18097
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 85-219 7.43e-32

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349970  Cd Length: 144  Bit Score: 113.43  E-value: 7.43e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  85 VAVENLDHDFNIGSIVRTANAMGARRVHVVG-----RKRWNRRGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVGVDNV 159
Cdd:cd18097     3 VVLDNLRSAHNVGSIFRTADAAGVEKIYLCGytptpPHPKVAKTALGAEESVPWEHFEDTLEAVRALKARGYTIIALETT 82

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 160 EGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:cd18097    83 ENSVPLHEARLPRPLALVLGNEVRGVSPEVLALCDAVVEIPMFGRKNSLNVAVAAAVALY 142
SpoU-like_TrmH cd18092
SAM-dependent tRNA methylase related to TrmH; TrmH catalyzes the transfer of the methyl group ...
 65-224 2.42e-26

SAM-dependent tRNA methylase related to TrmH; TrmH catalyzes the transfer of the methyl group from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of the ribose of the universally conserved guanosine 18 (G18) position in tRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349965  Cd Length: 162  Bit Score: 99.85  E-value: 2.42e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  65 RYWRMDAIradIAARSLPFEVAVENLDHDFNIGSIVRTANAMGARRVHVV---GRKRWNRRGAMVTDRYLPVDHRPEVGE 141
Cdd:cd18092     2 RLERIEEV---LARRTRDLTVVLENVHDPHNASAVLRTCDAFGVQDVHVIepkNKFKKNRGVAMGADKWLDVHRHDSTEE 78

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 142 LVDHCAREGLTLVGVDNVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMwAH 221
Cdd:cd18092    79 CLAALKEQGYRIVATSLSPDAVPLDELDYTRPTALVFGNEKDGVSEEALAAADERVYIPMYGFVESLNVSVAAAIIL-YE 157


                  ...
gi 2743938658 222 ASR 224
Cdd:cd18092   158 LQR 160
SpoU-like_family cd18082
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 88-220 1.25e-25

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349955  Cd Length: 145  Bit Score: 97.30  E-value: 1.25e-25
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  88 ENLDHDFNIGSIVRTANAMGARRVHVVG--RKRWNR---RGAMVTDRYLPVDHRPEVGELVDHCAREGLTLVGVDNVEGS 162
Cdd:cd18082     5 DNIRSPGNIGSIFRTADAFGVEKIYLVGptADIFDPkakRTSRGTHFSVPYERVDNFEEYLKSLKEEGYPLIGLELTDGS 84

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 163 IALEGAVL--PERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMWA 220
Cdd:cd18082    85 IPLSEFKFkkPKKIALIFGNERSGLSPELLALCDYTVHIPMSGKNSSLNVSVATGIALYE 144
SpoU-like_rRNA-MTase cd18095
SAM-dependent rRNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes ...
 95-219 2.78e-21

SAM-dependent rRNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349968  Cd Length: 143  Bit Score: 85.94  E-value: 2.78e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRVhVVGRK---RWN----R--RGAMVtdrYLPVDHRPEVGELVDHCAREGLTLVGVDnVEGSIAL 165
Cdd:cd18095    13 NLGTIIRTAAAFGVDGV-ILSKGtvdPYNpkvvRasMGALF---RLPIIRVDDLEELLEELKEAGYKVVAAD-LDGGSSL 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 2743938658 166 EGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:cd18095    88 YDLDLPKPVALVLGNEGNGLSDELLELCDKRVTIPMSGGVESLNVAVAAAILLY 141
SpoU COG0566
tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA ...
 62-220 4.69e-21

tRNA G18 (ribose-2'-O)-methylase SpoU [Translation, ribosomal structure and biogenesis]; tRNA G18 (ribose-2'-O)-methylase SpoU is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440332 [Multi-domain]  Cd Length: 265  Bit Score: 88.33  E-value: 4.69e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  62 DRYRYWRMDAIRADIAARslPFEVAVENL-DHdFNIGSIVRTANAMGARRVhVVGRKR---WNRR------GAMVtdrYL 131
Cdd:COG0566    97 RPPEYADLEDLLAEAGEP--PLLLVLDGVqDP-GNLGAILRSAAAFGVDGV-ILPKRRadpYNPKvvrasaGALF---HV 169

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 132 PVDHRPEVGELVDHCAREGLTLVGVDnVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVG 211
Cdd:COG0566   170 PVARVTNLADALEELKEAGFWVVGTD-LDGEASLYEVDLPGPVALVLGNEGKGLSRLVLEACDELVRIPMAGGVESLNVA 248


                  ....*....
gi 2743938658 212 HAAAIVMWA 220
Cdd:COG0566   249 VAAAILLYE 257
SpoU-like cd18098
SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase ...
 83-219 6.66e-21

SAM-dependent rRNA or tRNA methylase related to SpoU; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349971  Cd Length: 138  Bit Score: 85.01  E-value: 6.66e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  83 FEVAVENLDHDFNIGSIVRTANAMGARRVHVVGRKRwnRRGAMVTD-----RYLPVDHRPEVGELVDHCAReGLTLVGVD 157
Cdd:cd18098     1 FAIGIENPKTPKNVGTLWRAAGCLGASFVFTIGARY--KRRKQSTDtskawRHIPLFHYDDLEDLAEPLPF-GAVLVAVE 77

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 2743938658 158 NVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGstrSMNVGHAAAIVMW 219
Cdd:cd18098    78 LTEGATPLPDFKHPDRAVYLLGPEDGGLPQEVLARCHHVVYLPTRG---SLNVAVAGSIVLY 136
SpoU-like_TRM3-like cd18091
SAM-dependent tRNA methylase related to TRM3; Yeast tRNA (guanosine(18)-2'-O) ...
 90-219 1.72e-20

SAM-dependent tRNA methylase related to TRM3; Yeast tRNA (guanosine(18)-2'-O)-methyltransferase TRM3 catalyzes the formation of 2'-O-methylguanosine at position 18 (Gm18) in various tRNAs. TRM3 is similar to C-terminal domain of TAR (HIV-1) RNA binding protein 1 (TARBP1), a protein binding to TAR, which functions as a RNA regulatory signal by forming a stable stem-loop structure to which transactivator protein Tat binds. The role of TARBP1 is believed to be to disengage RNA polymerase II from TAR during transcriptional elongation. TRM3 and the C-terminal methyltransferase domain of TARBP1 are members of the SPOUT methyltransferase superfamily.


Pssm-ID: 349964  Cd Length: 145  Bit Score: 84.12  E-value: 1.72e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  90 LDHDFNIGSIVRTANAMGARRVhVVGRKRW-----NRRGAMVTDRYLP-VDHRPEvgELVDHCAR---EGLTLVGVDNVE 160
Cdd:cd18091     8 IDKPPNLGGLCRTCEIFGVSKL-VLPNLAVvedkqFKALSVSAEKWLPiEEVKPE--DLLPYLKEkkqEGYTIVGLEQTA 84

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 2743938658 161 GSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:cd18091    85 NSVSLHDFQFPKKTVLVLGNEKEGIPAELLSLLDVCVEIPQLGVIRSLNVHVSGAIAIY 143
SpoU-like_RlmB cd18103
SAM-dependent rRNA methylase related to RlmB; 23S rRNA-M2G2251-MTase RlmB catalyzes the ...
 90-220 4.35e-15

SAM-dependent rRNA methylase related to RlmB; 23S rRNA-M2G2251-MTase RlmB catalyzes the methylation of guanosine 2251, a modification conserved in the peptidyltransferase domain of 23S rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349976  Cd Length: 143  Bit Score: 69.72  E-value: 4.35e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  90 LDH--D-FNIGSIVRTANAMGARRVhVVGRKRWnrrgAMVTD----------RYLPVDHRPEVGELVDHCAREGLTLVGV 156
Cdd:cd18103     5 LDGitDpHNLGAIIRSAEAFGVDGV-IIPKRRS----APLTPtvakasagalEHLPIARVTNLARALEELKEAGFWIYGA 79

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 2743938658 157 DnVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMWA 220
Cdd:cd18103    80 D-GEAEKSLYDVDLTGPLALVLGSEGKGLRRLVLKNCDFLVKIPMAGKVDSLNVSVAAGIILYE 142
SpoU-like_RNA-MTase cd18104
SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes ...
 95-218 7.26e-12

SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349977  Cd Length: 146  Bit Score: 61.06  E-value: 7.26e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRVHVVGRKrwnrrgamvTDRYLPVDHRPEVG-------------ELVDHCAREGLTLVGVDnVEG 161
Cdd:cd18104    13 NLGAILRSADAAGADAVILCDPK---------TDLFNPNVIRASLGavftlpvaeasseETLAWLKENKIRILATT-PKA 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2743938658 162 SIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVM 218
Cdd:cd18104    83 EKLYYEADLRGPIAIVVGSESEGLSEFWLKAADERVRIPMAGQADSLNVSVAAAILL 139
rRNA_methyl_3 TIGR00186
rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases ...
 64-218 2.35e-10

rRNA methylase, putative, group 3; this is part of the trmH (spoU) family of rRNA methylases [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129290 [Multi-domain]  Cd Length: 237  Bit Score: 58.51  E-value: 2.35e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  64 YRYWRMDAIRADIAARSLPFEVAVENLDHDFNIGSIVRTANAMGARRVhVVGRKRWN------RRGAMVTDRYLPVDHRP 137
Cdd:TIGR00186  72 ILYKDLNDLYKTAKSKKQPFLLILDEITDPHNLGAILRTAEAFGVDGV-ILPKRRSAplnstvVKTSSGAVEYVPLARVT 150

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658 138 EVGELVDHCAREGLTLVGVDnVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIV 217
Cdd:TIGR00186 151 NLSRTITKLKESGFWTVGTD-LDAQDTLYQVKLTKPLALVVGNEGEGVSRLIKENCDFLIKIPMAGKVDSLNVSVAAGIL 229


                  .
gi 2743938658 218 M 218
Cdd:TIGR00186 230 L 230
SpoU-like_TrmJ cd18093
SAM-dependent tRNA methylase related to TrmJ; tRNA methyltransferase TrmJ catalyzes the methyl ...
 95-219 2.51e-10

SAM-dependent tRNA methylase related to TrmJ; tRNA methyltransferase TrmJ catalyzes the methyl transfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH at position 32 in both tRNASer1 and tRNAGln2. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349966  Cd Length: 153  Bit Score: 57.12  E-value: 2.51e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRVHVVGRKRW-----NRRGAMVTDRYLpvDHRPEVGELVDhcAREGLTLV-------------GV 156
Cdd:cd18093    13 NIGAVARAMKNFGLSDLRLVNPRCDdpeeaARALASGAEDVL--ENAKVYDTLEE--ALADCDLVvattarprglrrpLL 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 2743938658 157 DNVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:cd18093    89 TPRELAELLKEHAAGGKVALVFGREDSGLTNEELALCDLLVTIPTNPEYPSLNLAQAVAIVLY 151
SpoU-like_MRM1 cd18105
SAM-dependent rRNA methylase related to MRM1; MRM1 catalyzes the methylation of 2'-O-ribose ...
 95-220 8.20e-10

SAM-dependent rRNA methylase related to MRM1; MRM1 catalyzes the methylation of 2'-O-ribose residues G1145 to GmG residue of the mitochondrial 16S rRNA. MRM1 is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349978  Cd Length: 158  Bit Score: 55.60  E-value: 8.20e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRVhVVGRKRWNR---------RGAMvtdRYLPVDHRPEVGELVDHCAREGLTLVGVDNVEGSIAL 165
Cdd:cd18105    13 NLGAILRSAYFLGVDGV-VVSSKNSAPlspvvskasAGAL---ELMPIYSVDNLASFLKSSKENGWKVVGTSAPPSASSD 88

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 2743938658 166 EGAV--------LPERAC-LVFGSEASGLSEEMLAACEIVVAITQRGSTR-----SMNVGHAAAIVMWA 220
Cdd:cd18105    89 KKTIpanelselLLEKPTiLVLGNEGRGLRTNIKNLCDYLVSIPGGRSAEnpgvdSLNVSVAAGILLHS 157
SpoU-like_AviRb cd18107
SAM-dependent rRNA methylase related to AviRb; AviRb from Streptomyces viridochromogenes ...
 95-219 8.40e-10

SAM-dependent rRNA methylase related to AviRb; AviRb from Streptomyces viridochromogenes methylates the 2'-O atom of U2479 of the 23S ribosomal RNA. AviRb is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349980  Cd Length: 148  Bit Score: 55.47  E-value: 8.40e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRVHVVGRKR--WNR---RGAMVTDRYLPVDHRPEVGELVDHCARE-----GLTLVGVDNvEGSIA 164
Cdd:cd18107    13 NLGTIIRSADALGAHGLVVTGHAAdvYDPktiRASTGSLFSLPIVRVPSNRELEDWVEARkargtPLQLVGTDE-HGDHQ 91

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*
gi 2743938658 165 LEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:cd18107    92 IADHDFTRPTLLLIGNETAGLSAAWRELCDETVSIPMAGSASSLNAACAASIFLY 146
SpoU-like_TrmL cd18094
SAM-dependent tRNA methylase related to TrmL; tRNA (Um34/Cm34) methyltransferase TrmL ...
 95-219 1.52e-08

SAM-dependent tRNA methylase related to TrmL; tRNA (Um34/Cm34) methyltransferase TrmL catalyzes the methyl transfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH at position 34 in both tRNA(Leu)(CmAA) and tRNA(Leu)(cmnm5UmAA). It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349967  Cd Length: 145  Bit Score: 52.07  E-value: 1.52e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARrVHVVG------RKRWNRRGAMvtdrylpvDHRPEVgELVDH-CAREGLTLVGVDNV-----EGS 162
Cdd:cd18094    12 NTGNIARTCAATGAR-LHLIEplgfslDDKRLKRAGL--------DYWDHV-DLTVHdSWEAFLEALPPGRLflfttKGT 81

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 2743938658 163 IALEGAVLPERACLVFGSEASGLSEEMLAAC-EIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:cd18094    82 KPYTDFDFKPGDYLVFGRESTGLPEEILDAFpDRRLRIPMRPKVRSLNLSNSVAIVLY 139
SpoU-like_RNA-MTase cd18109
SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes ...
 95-218 1.25e-07

SAM-dependent RNA methylase related to SpoU-TrmH; RNA 2'-O ribose methyltransferase catalyzes the methyltransfer from S-adenosyl-L-methionine (AdoMet) to the 2'-OH group of ribose in tRNA or rRNA. It is part of the SpoU family of MTases, a subfamily of the SPOUT methyltransferase superfamily. The SPOUT methyltransferase superfamily is a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349982  Cd Length: 141  Bit Score: 49.07  E-value: 1.25e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRV------------HVVgrkrwnrRGAMVTDRYLPVDHRPEVGELVDHcaREGLTLVGVDnVEGS 162
Cdd:cd18109    13 NLGTIIRTADWFGIRQIicspdtvdpynpKVV-------QASMGSIFRVQIHYTDLPALLAEL--KKAFPVYGAD-LDGE 82

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2743938658 163 iALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGS-TRSMNVGHAAAIVM 218
Cdd:cd18109    83 -NLYEFTLPEKGILVMGNEGHGISPEVLKLLTHRLTIPRYGKgAESLNVAVATAILL 138
SpoU-like_NHR cd18108
Nosiheptide-resistance methyltransferase (NHR); Nosiheptide-resistance methyltransferase (NHR) ...
 95-220 3.97e-07

Nosiheptide-resistance methyltransferase (NHR); Nosiheptide-resistance methyltransferase (NHR) confers resistance to the thiazole antibiotic nosiheptide via catalyzing 2'O-methylation of 23S rRNA at the nucleotide A1067. NHR is a member of the SPOUT (SpoU-TrmD) methyltransferase (MTase) superfamily, a large class of S-adenosyl-L-methionine (AdoMet or SAM)-dependent RNA MTases which are structurally characterized by a deep trefoil knot.


Pssm-ID: 349981  Cd Length: 144  Bit Score: 47.86  E-value: 3.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  95 NIGSIVRTANAMGARRVHVVgrkrwNRRGAMVTDRYLPVDHRPEVGEL---------VDHCAREGLTLVGVDNVEGSIAL 165
Cdd:cd18108    13 NIGAIVRTSLALGAAGIVLV-----DSDLATVADRRLLRASRGYVFSLpvvladreeAVAFLRDNDIPLMTLDADGDVPV 87

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 2743938658 166 E--GAVlPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMWA 220
Cdd:cd18108    88 KelGDR-PDRLALVFGSEKGGPSGLFEEAAAGTVSIPMSSSTESLNVSVSAGIALHE 143
PRK11081 PRK11081
tRNA guanosine-2'-O-methyltransferase; Provisional
 65-219 2.04e-06

tRNA guanosine-2'-O-methyltransferase; Provisional


Pssm-ID: 236837 [Multi-domain]  Cd Length: 229  Bit Score: 46.91  E-value: 2.04e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 2743938658  65 RYWRmdaIRADIAARSLPFEVAVENLDHDFNIGSIVRTANAMGARRVHVV--GRKRWNRRG-AMVTDRYLPVDHRPEVGE 141
Cdd:PRK11081    5 RYAR---ICEMLARRQPDLTVCMEQVHKPHNVSAIIRTADAVGVHEVHAVwpGSRMRTMGStAAGSNSWVQVKTHRTIGD 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 2743938658 142 LVDHCAREGLTLVGVDNVEGSIALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:PRK11081   82 AVAHLKGQGMQILATHLSDTAVDFREIDYTRPTCILMGQEKTGISQEALALADQDIIIPMIGMVQSLNVSVASALILY 159
TrmL COG0219
tRNA(Leu) C34 or U34 (ribose-2'-O)-methylase TrmL, contains SPOUT domain [Translation, ...
 176-217 2.95e-06

tRNA(Leu) C34 or U34 (ribose-2'-O)-methylase TrmL, contains SPOUT domain [Translation, ribosomal structure and biogenesis]; tRNA(Leu) C34 or U34 (ribose-2'-O)-methylase TrmL, contains SPOUT domain is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 439989  Cd Length: 153  Bit Score: 45.79  E-value: 2.95e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|...
gi 2743938658 176 LVFGSEASGLSEEMLAA-CEIVVAITQRGSTRSMNVGHAAAIV 217
Cdd:COG0219    97 LLFGRETAGLPEEVLAApADQRLRIPMRPGVRSLNLSNAVAIV 139
PRK10864 PRK10864
putative methyltransferase; Provisional
 144-218 4.73e-05

putative methyltransferase; Provisional


Pssm-ID: 236779 [Multi-domain]  Cd Length: 346  Bit Score: 43.61  E-value: 4.73e-05
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 2743938658 144 DHCAREGLTLVGVDNVEGSiALEGAVLPERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVM 218
Cdd:PRK10864  264 DDFRQAGYTIVTTSSHKGT-PLFKASLPAKMVLVLGQEYDGLSDAARQQGDLSVSIDGTGNVESLNVSVATGVLL 337
TrmJ COG0565
tRNA C32,U32 (ribose-2'-O)-methylase TrmJ or a related methyltransferase [Translation, ...
 172-219 6.61e-04

tRNA C32,U32 (ribose-2'-O)-methylase TrmJ or a related methyltransferase [Translation, ribosomal structure and biogenesis]; tRNA C32,U32 (ribose-2'-O)-methylase TrmJ or a related methyltransferase is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 440331 [Multi-domain]  Cd Length: 237  Bit Score: 39.71  E-value: 6.61e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 2743938658 172 ERACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMW 219
Cdd:COG0565   106 GKVALVFGRERSGLTNEELALCDALVTIPTNPEYPSLNLAQAVQVVAY 153
PRK10433 PRK10433
putative RNA methyltransferase; Provisional
 173-223 1.03e-03

putative RNA methyltransferase; Provisional


Pssm-ID: 236693  Cd Length: 228  Bit Score: 39.20  E-value: 1.03e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 2743938658 173 RACLVFGSEASGLSEEMLAACEIVVAITQRGSTRSMNVGHAAAIVMWAHAS 223
Cdd:PRK10433  107 HAALVFGREDSGLTNEELALADVLTGVPMAADYPSLNLGQAVMVYCYQLAG 157
 
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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