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Conserved domains on  [gi|304555603|ref|NP_001182134|]
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tRNA (uracil-5-)-methyltransferase homolog A isoform 4 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmA super family cl43665
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 168-538 1.28e-45

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


The actual alignment was detected with superfamily member COG2265:

Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 164.96  E-value: 1.28e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 168 VPYTEQLEQKRLECERVLQKLAKEIGntnrallpwlllqrqqhnkacCPLEGVKPSPQQTEYRNKCEFlvgvGVDGKDNT 247
Cdd:COG2265   81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 248 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtssrgqamaiayfhpqk 326
Cdd:COG2265  136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 327 lsseevaglkaslvchfmegpgkasgvtslyfveegqrktpsqeglplehmAGDQCIQEDLLGLTFRISPHAFFQVNTPA 406
Cdd:COG2265  189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 407 AEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTN------------------- 467
Cdd:COG2265  218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNglknvefvagdleevlpel 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 468 ------------------DSKVILAIRKAeNIKRLLYVSCNP----RaamgnfvDLCRAPSNRvkgtpFHPVKAVAVDLF 525
Cdd:COG2265  298 lwggrpdvvvldppragaGPEVLEALAAL-GPRRIVYVSCNPatlaR-------DLALLVEGG-----YRLEKVQPVDMF 364

                        410
                 ....*....|...
gi 304555603 526 PQTPHCEMLILFE 538
Cdd:COG2265  365 PHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 58-136 1.91e-39

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


:

Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 138.53  E-value: 1.91e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 304555603  58 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQSHKIKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLARP 136
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 168-538 1.28e-45

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 164.96  E-value: 1.28e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 168 VPYTEQLEQKRLECERVLQKLAKEIGntnrallpwlllqrqqhnkacCPLEGVKPSPQQTEYRNKCEFlvgvGVDGKDNT 247
Cdd:COG2265   81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 248 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtssrgqamaiayfhpqk 326
Cdd:COG2265  136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 327 lsseevaglkaslvchfmegpgkasgvtslyfveegqrktpsqeglplehmAGDQCIQEDLLGLTFRISPHAFFQVNTPA 406
Cdd:COG2265  189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 407 AEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTN------------------- 467
Cdd:COG2265  218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNglknvefvagdleevlpel 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 468 ------------------DSKVILAIRKAeNIKRLLYVSCNP----RaamgnfvDLCRAPSNRvkgtpFHPVKAVAVDLF 525
Cdd:COG2265  298 lwggrpdvvvldppragaGPEVLEALAAL-GPRRIVYVSCNPatlaR-------DLALLVEGG-----YRLEKVQPVDMF 364

                        410
                 ....*....|...
gi 304555603 526 PQTPHCEMLILFE 538
Cdd:COG2265  365 PHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 58-136 1.91e-39

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 138.53  E-value: 1.91e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 304555603  58 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQSHKIKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLARP 136
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 204-532 3.74e-26

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 111.07  E-value: 3.74e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  204 LLQRQQHNKaccpLEGVKPSPQQTE----YRNKCEFLVGVGVDGKdntvgCRLGKYKGGT--------CAVAAPfdtvhi 271
Cdd:TIGR00479  88 LLERIGKFV----SEPIEDVPTIGDdpwgYRNKARLSLGRSPSGQ-----LQAGFYQKGShdivdvkqCPVQAP------ 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  272 peATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSSRGQAMAIAyFHPQKLSSEEVAGLKASLVCHFMEGPGKAS 351
Cdd:TIGR00479 153 --ALNALLPKVRAILENFGASRYLEHKELGQARHGVLRIGRHTGELSSV-DRTALERFPHKEELDLYLQPDSPDVKSICQ 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  352 GVTSlyfveegqRKTPSQEGLPLEHMAGDQCIQEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCC 431
Cdd:TIGR00479 230 NINP--------EKTNVIFGEETEVIAGEMPIYDKSGDLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYC 301

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  432 GTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTN--------------------------------------DSKVIL 473
Cdd:TIGR00479 302 GMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNgianvtfyhgtletvlpkqpwagngfdkvlldpprkgcAAGVLR 381

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 304555603  474 AIRKAENiKRLLYVSCNPRAAMGNFVDLCRAPSNRVKGTPfhpvkavaVDLFPQTPHCE 532
Cdd:TIGR00479 382 TIIKLKP-ERIVYVSCNPATLARDLEALCKAGYTIARVQP--------VDMFPHTGHVE 431
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
375-539 1.04e-19

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 90.31  E-value: 1.04e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 375 EHMA---GDQCI--------QEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPK 443
Cdd:PRK03522 115 VHMAileGEEEIflteqqalPERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSMWDLFCGVGGFGLHCATP 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 444 VKRVVGIELCQEAVEDARMNA----LTN------DS-KVILA----------------IRKA-------ENIKRLLYVSC 489
Cdd:PRK03522 195 GMQLTGIEISAEAIACAKQSAaelgLTNvqfqalDStQFATAqgevpdlvlvnpprrgIGKElcdylsqMAPRFILYSSC 274

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 304555603 490 NPrAAMGNfvDLCRAPSnrvkgtpFHPVKAVAVDLFPQTPHCEMLILFER 539
Cdd:PRK03522 275 NA-QTMAK--DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 426-481 5.66e-08

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 50.64  E-value: 5.66e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 304555603  426 VLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDARMNALTNDSKVILAIRKAENI 481
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGGaRVTGVDLSPEMLERARERAAEAGLNVEFVQGDAEDL 57
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
69-139 2.12e-06

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.86  E-value: 2.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  69 NVPRHASFSDVRRFLGRFGL-QSHKI---------KLFGqppcaFVTFRSAAERDKALRVLHGALWKGCPLSVRLARPKA 138
Cdd:COG0724    8 NLPYSVTEEDLRELFSEYGEvTSVKLitdretgrsRGFG-----FVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82


                 .
gi 304555603 139 D 139
Cdd:COG0724   83 E 83
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 425-467 3.01e-05

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: 43.19  E-value: 3.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 304555603 425 TVLDVCCGTGTIGLALA-PKVKRVVGIELCQEAVEDARMNALTN 467
Cdd:cd02440    1 RVLDLGCGTGALALALAsGPGARVTGVDISPVALELARKAAAAL 44
RRM smart00360
RNA recognition motif;
69-131 1.40e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 1.40e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 304555603    69 NVPRHASFSDVRRFLGRFG----LQSHKIKLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGCPLSV 131
Cdd:smart00360   6 NLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSkGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 168-538 1.28e-45

tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure and biogenesis]; tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 441866 [Multi-domain]  Cd Length: 377  Bit Score: 164.96  E-value: 1.28e-45
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 168 VPYTEQLEQKRLECERVLQKLAKEIGntnrallpwlllqrqqhnkacCPLEGVKPSPQQTEYRNKCEFlvgvGVDGKDNT 247
Cdd:COG2265   81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 248 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtssrgqamaiayfhpqk 326
Cdd:COG2265  136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 327 lsseevaglkaslvchfmegpgkasgvtslyfveegqrktpsqeglplehmAGDQCIQEDLLGLTFRISPHAFFQVNTPA 406
Cdd:COG2265  189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 407 AEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTN------------------- 467
Cdd:COG2265  218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNglknvefvagdleevlpel 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 468 ------------------DSKVILAIRKAeNIKRLLYVSCNP----RaamgnfvDLCRAPSNRvkgtpFHPVKAVAVDLF 525
Cdd:COG2265  298 lwggrpdvvvldppragaGPEVLEALAAL-GPRRIVYVSCNPatlaR-------DLALLVEGG-----YRLEKVQPVDMF 364

                        410
                 ....*....|...
gi 304555603 526 PQTPHCEMLILFE 538
Cdd:COG2265  365 PHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 58-136 1.91e-39

RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and similar proteins; This subfamily corresponds to the RRM of TRMT2A, also known as HpaII tiny fragments locus 9c protein (HTF9C), a novel cell cycle regulated protein. It is an independent biologic factor expressed in tumors associated with clinical outcome in HER2 expressing breast cancer. The function of TRMT2A remains unclear although by sequence homology it has a RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), related to RNA methyltransferases.


Pssm-ID: 409873 [Multi-domain]  Cd Length: 79  Bit Score: 138.53  E-value: 1.91e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 304555603  58 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQSHKIKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLARP 136
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 204-532 3.74e-26

23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA methyltransferases by homology to the TrmA family. The member from E. coli has now been shown to act as the 23S RNA methyltransferase for the conserved U1939. The gene is now designated rumA and was previously designated ygcA. [Protein synthesis, tRNA and rRNA base modification]


Pssm-ID: 129571 [Multi-domain]  Cd Length: 431  Bit Score: 111.07  E-value: 3.74e-26
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  204 LLQRQQHNKaccpLEGVKPSPQQTE----YRNKCEFLVGVGVDGKdntvgCRLGKYKGGT--------CAVAAPfdtvhi 271
Cdd:TIGR00479  88 LLERIGKFV----SEPIEDVPTIGDdpwgYRNKARLSLGRSPSGQ-----LQAGFYQKGShdivdvkqCPVQAP------ 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  272 peATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSSRGQAMAIAyFHPQKLSSEEVAGLKASLVCHFMEGPGKAS 351
Cdd:TIGR00479 153 --ALNALLPKVRAILENFGASRYLEHKELGQARHGVLRIGRHTGELSSV-DRTALERFPHKEELDLYLQPDSPDVKSICQ 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  352 GVTSlyfveegqRKTPSQEGLPLEHMAGDQCIQEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCC 431
Cdd:TIGR00479 230 NINP--------EKTNVIFGEETEVIAGEMPIYDKSGDLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYC 301

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  432 GTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTN--------------------------------------DSKVIL 473
Cdd:TIGR00479 302 GMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNgianvtfyhgtletvlpkqpwagngfdkvlldpprkgcAAGVLR 381

                         330       340       350       360       370
                  ....*....|....*....|....*....|....*....|....*....|....*....
gi 304555603  474 AIRKAENiKRLLYVSCNPRAAMGNFVDLCRAPSNRVKGTPfhpvkavaVDLFPQTPHCE 532
Cdd:TIGR00479 382 TIIKLKP-ERIVYVSCNPATLARDLEALCKAGYTIARVQP--------VDMFPHTGHVE 431
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
375-539 1.04e-19

23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 90.31  E-value: 1.04e-19
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 375 EHMA---GDQCI--------QEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPK 443
Cdd:PRK03522 115 VHMAileGEEEIflteqqalPERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSMWDLFCGVGGFGLHCATP 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 444 VKRVVGIELCQEAVEDARMNA----LTN------DS-KVILA----------------IRKA-------ENIKRLLYVSC 489
Cdd:PRK03522 195 GMQLTGIEISAEAIACAKQSAaelgLTNvqfqalDStQFATAqgevpdlvlvnpprrgIGKElcdylsqMAPRFILYSSC 274

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|
gi 304555603 490 NPrAAMGNfvDLCRAPSnrvkgtpFHPVKAVAVDLFPQTPHCEMLILFER 539
Cdd:PRK03522 275 NA-QTMAK--DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
389-539 4.24e-12

23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 68.26  E-value: 4.24e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 389 GLTFRISPHAFFQVNTPAAEVLytVIQ--EWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALT 466
Cdd:PRK13168 264 GLRLAFSPRDFIQVNAQVNQKM--VARalEWLDPQPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARR 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 467 ND-------------------------SKVIL------------AIRKAeNIKRLLYVSCNPraamgnfVDLCRAPSNRV 509
Cdd:PRK13168 342 NGldnvtfyhanleedftdqpwalggfDKVLLdppragaaevmqALAKL-GPKRIVYVSCNP-------ATLARDAGVLV 413

                        170       180       190
                 ....*....|....*....|....*....|
gi 304555603 510 KGtPFHPVKAVAVDLFPQTPHCEMLILFER 539
Cdd:PRK13168 414 EA-GYRLKRAGMLDMFPHTGHVESMALFER 442
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 417-467 2.74e-09

tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) A37 N6-methylase TrmN6 is part of the Pathway/BioSystem: tRNA modification


Pssm-ID: 443299 [Multi-domain]  Cd Length: 238  Bit Score: 57.85  E-value: 2.74e-09
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|...
gi 304555603 417 WAQLDGGSTVLDVCCGTGTIGLALAPKVK--RVVGIELCQEAVEDARMNALTN 467
Cdd:COG4123   32 FAPVKKGGRVLDLGTGTGVIALMLAQRSPgaRITGVEIQPEAAELARRNVALN 84
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 369-464 3.03e-09

Methylase of polypeptide chain release factors [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 58.24  E-value: 3.03e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 369 QEGLPLEHMAGdqciQEDLLGLTFRISPHAFfqV---NTpaaEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALA---P 442
Cdd:COG2890   65 AAGEPLAYILG----EAEFYGLEFKVDPGVL--IprpET---EELVELALALLPAGAPPRVLDLGTGSGAIALALAkerP 135

                         90       100
                 ....*....|....*....|..
gi 304555603 443 KVkRVVGIELCQEAVEDARMNA 464
Cdd:COG2890  136 DA-RVTAVDISPDALAVARRNA 156
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
406-461 2.90e-08

Predicted methyltransferase, contains TPR repeat [General function prediction only];


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 53.85  E-value: 2.90e-08
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 304555603 406 AAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDAR 461
Cdd:COG4976   30 APALLAEELLARLPPGPFGRVLDLGCGTGLLGEALRPRGYRLTGVDLSEEMLAKAR 85
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 416-464 3.87e-08

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: 52.30  E-value: 3.87e-08
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*....
gi 304555603 416 EWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNA 464
Cdd:COG2226   16 AALGLRPGARVLDLGCGTGRLALALAERGARVTGVDISPEMLELARERA 64
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
401-491 4.77e-08

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 53.37  E-value: 4.77e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 401 QVNTP---AAEVLYTviqewAQLDG---GSTVLDVCCGTGTIGLALAPK-VKRVVGIELCQEAVEDARMNA--LTNDSKV 471
Cdd:COG2263   23 QYPTPaelAAELLHL-----AYLRGdieGKTVLDLGCGTGMLAIGAALLgAKKVVGVDIDPEALEIARENAerLGVRVDF 97

                         90       100
                 ....*....|....*....|.
gi 304555603 472 ILA-IRKAENIKRLLYVSCNP 491
Cdd:COG2263   98 IRAdVTRIPLGGSVDTVVMNP 118
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 426-481 5.66e-08

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 50.64  E-value: 5.66e-08
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 304555603  426 VLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDARMNALTNDSKVILAIRKAENI 481
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGGaRVTGVDLSPEMLERARERAAEAGLNVEFVQGDAEDL 57
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 370-464 1.06e-07

N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 53.63  E-value: 1.06e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 370 EGLPLEHMAGdqciQEDLLGLTFRISPHAFfqVNTPAAEVLytViqEWA----QLDGGSTVLDVCCGTGTIGLALA---P 442
Cdd:PRK09328  62 AGEPLQYILG----EAEFWGLDFKVSPGVL--IPRPETEEL--V--EWAlealLLKEPLRVLDLGTGSGAIALALAkerP 131

                         90       100
                 ....*....|....*....|..
gi 304555603 443 KVkRVVGIELCQEAVEDARMNA 464
Cdd:PRK09328 132 DA-EVTAVDISPEALAVARRNA 152
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 410-464 4.04e-07

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: 49.25  E-value: 4.04e-07
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*
gi 304555603 410 LYTVIQEWaqLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNA 464
Cdd:COG2227   14 LAALLARL--LPAGGRVLDVGCGTGRLALALARRGADVTGVDISPEALEIARERA 66
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 69-132 8.29e-07

RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), is a highly abundant domain in eukaryotes found in proteins involved in post-transcriptional gene expression processes including mRNA and rRNA processing, RNA export, and RNA stability. This domain is 90 amino acids in length and consists of a four-stranded beta-sheet packed against two alpha-helices. RRM usually interacts with ssRNA, but is also known to interact with ssDNA as well as proteins. RRM binds a variable number of nucleotides, ranging from two to eight. The active site includes three aromatic side-chains located within the conserved RNP1 and RNP2 motifs of the domain. The RRM domain is found in a variety heterogeneous nuclear ribonucleoproteins (hnRNPs), proteins implicated in regulation of alternative splicing, and protein components of small nuclear ribonucleoproteins (snRNPs).


Pssm-ID: 409669 [Multi-domain]  Cd Length: 72  Bit Score: 46.51  E-value: 8.29e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 304555603  69 NVPRHASFSDVRRFLGRFG-LQSHKI---KLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVR 132
Cdd:cd00590    5 NLPPDTTEEDLRELFSKFGeVVSVRIvrdRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 69-131 1.43e-06

RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM1 of RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein), It serves as a bridging factor between the U11 and U12 snRNPs. It contains two repeats of RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions.


Pssm-ID: 409684 [Multi-domain]  Cd Length: 73  Bit Score: 46.09  E-value: 1.43e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 304555603  69 NVPRHASFSDVRRFLGRFGLQShkIKLFGQPP----CAFVTFRSAAERDKALRVLHGALWKGCPLSV 131
Cdd:cd12238    6 HLPPELSEDDKEDLLKHFGATS--VRVMKRRGklkhTAFATFDNEQAASKALSRLHQLKILGKRLVV 70
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
69-139 2.12e-06

RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 45.86  E-value: 2.12e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  69 NVPRHASFSDVRRFLGRFGL-QSHKI---------KLFGqppcaFVTFRSAAERDKALRVLHGALWKGCPLSVRLARPKA 138
Cdd:COG0724    8 NLPYSVTEEDLRELFSEYGEvTSVKLitdretgrsRGFG-----FVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82


                 .
gi 304555603 139 D 139
Cdd:COG0724   83 E 83
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 405-464 2.49e-06

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


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 48.37  E-value: 2.49e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 304555603 405 PAAEVLYTVIQEwaqLDGGSTVLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDARMNA 464
Cdd:COG0500   12 PGLAALLALLER---LPKGGRVLDLGCGTGRNLLALAARFGgRVIGIDLSPEAIALARARA 69
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 420-464 7.18e-06

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 46.26  E-value: 7.18e-06
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 304555603  420 LDGGSTVLDVCCGTGTIGLALAPKV---KRVVGIELCQEAVEDARMNA 464
Cdd:pfam13847   1 IDKGMRVLDLGCGTGHLSFELAEELgpnAEVVGIDISEEAIEKARENA 48
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 417-467 1.43e-05

16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA G1207 methylase RsmC is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 442062 [Multi-domain]  Cd Length: 191  Bit Score: 45.95  E-value: 1.43e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 304555603 417 WAQLDGGS-------------TVLDVCCGTGTIGLALA--PKVKRVVGIELCQEAVEDARMNALTN 467
Cdd:COG2813   31 RDRLDIGTrlllehlpeplggRVLDLGCGYGVIGLALAkrNPEARVTLVDVNARAVELARANAAAN 96
PRK14968 PRK14968
putative methyltransferase; Provisional
 423-470 1.45e-05

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 46.05  E-value: 1.45e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 304555603 423 GSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNDSK 470
Cdd:PRK14968  24 GDRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIR 71
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
422-461 2.17e-05

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 43.27  E-value: 2.17e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|..
gi 304555603 422 GGSTVLDVCCGTGTIGLALAPKVK--RVVGIELCQEAVEDAR 461
Cdd:COG4106    1 PPRRVLDLGCGTGRLTALLAERFPgaRVTGVDLSPEMLARAR 42
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 405-461 2.95e-05

Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport and metabolism];


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 44.54  E-value: 2.95e-05
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 304555603 405 PAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDAR 461
Cdd:COG2230   34 EAQEAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGvRVTGVTLSPEQLEYAR 91
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 425-467 3.01e-05

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: 43.19  E-value: 3.01e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 304555603 425 TVLDVCCGTGTIGLALA-PKVKRVVGIELCQEAVEDARMNALTN 467
Cdd:cd02440    1 RVLDLGCGTGALALALAsGPGARVTGVDISPVALELARKAAAAL 44
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 418-474 5.92e-05

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: 43.78  E-value: 5.92e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 418 AQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMN---ALTNDSKVILA 474
Cdd:COG1041   22 AGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENlehYGYEDADVIRG 81
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 416-461 7.06e-05

ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of methyltransferases involved in the biosynthesis of menaquinone and ubiqinone. Some members such as the UbiE enzyme from E. coli are believed to act in both pathways, while others may act in only the menaquinone pathway. These methyltransferases are members of the UbiE/CoQ family of methyltransferases (pfam01209) which also contains ubiquinone methyltransferases and other methyltransferases. Members of this clade include a wide distribution of bacteria and eukaryotes, but no archaea. An outgroup for this clade is provided by the phosphatidylethanolamine methyltransferase (EC 2.1.1.17) from Rhodobacter sphaeroides. Note that a number of non-orthologous genes which are members of pfam03737 have been erroneously annotated as MenG methyltransferases. [Biosynthesis of cofactors, prosthetic groups, and carriers, Menaquinone and ubiquinone]


Pssm-ID: 273884 [Multi-domain]  Cd Length: 223  Bit Score: 44.56  E-value: 7.06e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 304555603  416 EWAQLDGGSTVLDVCCGTGTIGLALA---PKVKRVVGIELCQEAVEDAR 461
Cdd:TIGR01934  33 KLIGVFKGQKVLDVACGTGDLAIELAksaPDRGKVTGVDFSSEMLEVAK 81
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 64-134 1.27e-04

RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; This subfamily corresponds to the RRM2 of RBM40 and the RRM of RBM41. RBM40, also known as RNA-binding region-containing protein 3 (RNPC3) or U11/U12 small nuclear ribonucleoprotein 65 kDa protein (U11/U12-65K protein). It serves as a bridging factor between the U11 and U12 snRNPs. It contains two RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), connected by a linker that includes a proline-rich region. It binds to the U11-associated 59K protein via its RRM1 and employs the RRM2 to bind hairpin III of the U12 small nuclear RNA (snRNA). The proline-rich region might be involved in protein-protein interactions. RBM41 contains only one RRM. Its biological function remains unclear.


Pssm-ID: 409685 [Multi-domain]  Cd Length: 82  Bit Score: 40.67  E-value: 1.27e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  64 KLELQNVPRHASFSDVRRFLGRFgLQSHK-------IKLF------GQppcAFVTFRSAAERDKALRVLHGALWKGCPLS 130
Cdd:cd12239    3 RLYVKNLSKRVSEKDLKYIFGRF-VDSSSeeknmfdIRLMtegrmkGQ---AFITFPSEELAEKALNLTNGYVLHGKPMV 78


                 ....
gi 304555603 131 VRLA 134
Cdd:cd12239   79 VQFA 82
RRM smart00360
RNA recognition motif;
69-131 1.40e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 1.40e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 304555603    69 NVPRHASFSDVRRFLGRFG----LQSHKIKLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGCPLSV 131
Cdd:smart00360   6 NLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSkGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
 390-539 2.01e-04

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 43.66  E-value: 2.01e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 390 LTFRISPHAFFQVNTpaaevlyTVIQ---EWAQ---LDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDA--- 460
Cdd:PRK05031 175 FIYRQVENSFTQPNA-------AVNEkmlEWALdatKGSKGDLLELYCGNGNFTLALARNFRRVLATEISKPSVAAAqyn 247

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603 461 ------------RMNA--LTN---------------------------------DSKVILAIRKAENIkrlLYVSCNPRA 493
Cdd:PRK05031 248 iaangidnvqiiRMSAeeFTQamngvrefnrlkgidlksynfstifvdppraglDDETLKLVQAYERI---LYISCNPET 324

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 304555603 494 AMGNFVDLCRApsnrvkgtpfHPVKAVAV-DLFPQTPHCEMLILFER 539
Cdd:PRK05031 325 LCENLETLSQT----------HKVERFALfDQFPYTHHMECGVLLEK 361
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 427-474 3.00e-04

Methyltransferase domain; Members of this family are SAM dependent methyltransferases.


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 39.96  E-value: 3.00e-04
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*...
gi 304555603  427 LDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNDSKVILA 474
Cdd:pfam08241   1 LDVGCGTGLLTELLARLGARVTGVDISPEMLELAREKAPREGLTFVVG 48
PRK14967 PRK14967
putative methyltransferase; Provisional
 420-465 3.62e-04

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 42.35  E-value: 3.62e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 304555603 420 LDGGSTVLDVCCGTGTIGLALAPK-VKRVVGIELCQEAVEDARMNAL 465
Cdd:PRK14967  34 LGPGRRVLDLCTGSGALAVAAAAAgAGSVTAVDISRRAVRSARLNAL 80
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 416-450 4.48e-04

bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol methylase UbiE;


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 42.06  E-value: 4.48e-04
                         10        20        30
                 ....*....|....*....|....*....|....*...
gi 304555603 416 EWAQLDGGSTVLDVCCGTGTIGLALA---PKVKRVVGI 450
Cdd:PRK00216  45 KWLGVRPGDKVLDLACGTGDLAIALAkavGKTGEVVGL 82
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 91-135 9.44e-04

RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; This subfamily corresponds to the RRM of RBM18, a putative RNA-binding protein containing a well-conserved RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). The biological role of RBM18 remains unclear.


Pssm-ID: 409791 [Multi-domain]  Cd Length: 80  Bit Score: 38.05  E-value: 9.44e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 304555603  91 HKI-KLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLAR 135
Cdd:cd12355   34 HKTgPLKGQPrGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWAH 80
PCMT pfam01135
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);
416-463 1.00e-03

Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);


Pssm-ID: 395902 [Multi-domain]  Cd Length: 205  Bit Score: 40.81  E-value: 1.00e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|.
gi 304555603  416 EWAQLDGGSTVLDVCCGTGTIGLALAPKVK---RVVGIELCQEAVEDARMN 463
Cdd:pfam01135  67 ELLELKPGMRVLEIGSGSGYLTACFARMVGevgRVVSIEHIPELVEIARRN 117
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 64-132 1.08e-03

RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding proteins and plant flowering time control protein FCA; This subfamily corresponds to the RRM1 and RRM2 domains of the CUGBP1 and ETR-3-like factors (CELF) as well as plant flowering time control protein FCA. CELF, also termed BRUNOL (Bruno-like) proteins, is a family of structurally related RNA-binding proteins involved in regulation of pre-mRNA splicing in the nucleus, and control of mRNA translation and deadenylation in the cytoplasm. The family contains six members: CELF-1 (also known as BRUNOL-2, CUG-BP1, NAPOR, EDEN-BP), CELF-2 (also known as BRUNOL-3, ETR-3, CUG-BP2, NAPOR-2), CELF-3 (also known as BRUNOL-1, TNRC4, ETR-1, CAGH4, ER DA4), CELF-4 (BRUNOL-4), CELF-5 (BRUNOL-5) and CELF-6 (BRUNOL-6). They all contain three highly conserved RNA recognition motifs (RRMs), also known as RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains): two consecutive RRMs (RRM1 and RRM2) situated in the N-terminal region followed by a linker region and the third RRM (RRM3) close to the C-terminus of the protein. The low sequence conservation of the linker region is highly suggestive of a large variety in the co-factors that associate with the various CELF family members. Based on both, sequence similarity and function, the CELF family can be divided into two subfamilies, the first containing CELFs 1 and 2, and the second containing CELFs 3, 4, 5, and 6. The different CELF proteins may act through different sites on at least some substrates. Furthermore, CELF proteins may interact with each other in varying combinations to influence alternative splicing in different contexts. This subfamily also includes plant flowering time control protein FCA that functions in the posttranscriptional regulation of transcripts involved in the flowering process. FCA contains two RRMs, and a WW protein interaction domain.


Pssm-ID: 409796 [Multi-domain]  Cd Length: 77  Bit Score: 37.99  E-value: 1.08e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 304555603  64 KLELQNVPRHASFSDVRRFLGRFG----LQSHKIKLFGQPP-CAFVTFRSAAERDKALRVLHGA-LWKGC--PLSVR 132
Cdd:cd12361    1 KLFVGMIPKTASEEDVRPLFEQFGnieeVQILRDKQTGQSKgCAFVTFSTREEALRAIEALHNKkTMPGCssPLQVK 77
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
 101-135 1.71e-03

RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This subfamily corresponds to the RRM of NELF-E, also termed RNA-binding protein RD. NELF-E is the RNA-binding subunit of cellular negative transcription elongation factor NELF (negative elongation factor) involved in transcriptional regulation of HIV-1 by binding to the stem of the viral transactivation-response element (TAR) RNA which is synthesized by cellular RNA polymerase II at the viral long terminal repeat. NELF is a heterotetrameric protein consisting of NELF A, B, C or the splice variant D, and E. NELF-E contains an RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain). It plays a role in the control of HIV transcription by binding to TAR RNA. In addition, NELF-E is associated with the NELF-B subunit, probably via a leucine zipper motif.


Pssm-ID: 409746 [Multi-domain]  Cd Length: 75  Bit Score: 37.30  E-value: 1.71e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 304555603 101 CAFVTFRSAAERDKALRVLHGALWKGCPLSVRLAR 135
Cdd:cd12305   40 CAFVTFEKMESADQAIAELNGTTVEGVQLKVSIAR 74
hemK_fam TIGR00536
HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme ...
 370-467 1.91e-03

HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme biosynthesis and originally suggested to be protoporphyrinogen oxidase. Functional analysis of the nearest homolog in Saccharomyces cerevisiae, YNL063w, finds it is not protoporphyrinogen oxidase and sequence analysis suggests that HemK homologs have S-adenosyl-methionine-dependent methyltransferase activity (Medline 99237242). Homologs are found, usually in a single copy, in nearly all completed genomes, but varying somewhat in apparent domain architecture. Both E. coli and H. influenzae have two members rather than one. The members from the Mycoplasmas have an additional C-terminal domain. [Protein fate, Protein modification and repair]


Pssm-ID: 273125 [Multi-domain]  Cd Length: 284  Bit Score: 40.41  E-value: 1.91e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  370 EGLPLEHMAGdqciQEDLLGLTFRISPHaffqVNTPAAEVLYTVIQEWAQL---DGGSTVLDVCCGTGTIGLALAPKV-- 444
Cdd:TIGR00536  67 KGVPVAYLLG----SKEFYGLEFFVNEH----VLIPRPETEELVEKALASLisqPPILHILDLGTGSGCIALALAYEFpn 138

                          90       100
                  ....*....|....*....|...
gi 304555603  445 KRVVGIELCQEAVEDARMNALTN 467
Cdd:TIGR00536 139 AEVIAVDISPDALAVAEENAEKN 161
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 59-136 2.52e-03

RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This subgroup corresponds to the RRM of SR140 (also termed U2 snRNP-associated SURP motif-containing protein orU2SURP, or 140 kDa Ser/Arg-rich domain protein) which is a putative splicing factor mainly found in higher eukaryotes. Although it is initially identified as one of the 17S U2 snRNP-associated proteins, the molecular and physiological function of SR140 remains unclear. SR140 contains an N-terminal RNA recognition motif (RRM), also termed RBD (RNA binding domain) or RNP (ribonucleoprotein domain), a SWAP/SURP domain that is found in a number of pre-mRNA splicing factors in the middle region, and a C-terminal arginine/serine-rich domain (RS domain).


Pssm-ID: 409670 [Multi-domain]  Cd Length: 84  Bit Score: 37.27  E-value: 2.52e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 304555603  59 TSEIFkleLQNVPRHASFSDVRRFLGRFG-LQSHKIkLFGQPP--------CAFVTFRSAAERDKALRVLHGALWKGCPL 129
Cdd:cd12223    1 TTNLY---VGNLPPSVTEEVLLREFGRFGpLASVKI-MWPRTEeerrrnrnCGFVAFMSRADAERAMRELNGKDVMGYEL 76


                 ....*..
gi 304555603 130 SVRLARP 136
Cdd:cd12223   77 KLGWGKA 83
PrmA pfam06325
Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal ...
 416-467 3.84e-03

Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal protein L11 methyltransferase (EC:2.1.1.-) sequences.


Pssm-ID: 428888 [Multi-domain]  Cd Length: 294  Bit Score: 39.56  E-value: 3.84e-03
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 304555603  416 EW--AQLDGGSTVLDVCCGTGTIGLAlAPK--VKRVVGIELCQEAVEDARMNALTN 467
Cdd:pfam06325 153 EAleRLVKPGESVLDVGCGSGILAIA-ALKlgAKKVVGVDIDPVAVRAAKENAELN 207
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 65-117 5.15e-03

RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein family, epithelial splicing regulatory proteins (ESRPs), Drosophila RNA-binding protein Fusilli, RNA-binding protein 12 (RBM12) and similar proteins; The family includes RRM domains in the hnRNP H protein family, G-rich sequence factor 1 (GRSF-1), ESRPs (also termed RBM35), Drosophila Fusilli, RBM12 (also termed SWAN), RBM12B, RBM19 (also termed RBD-1) and similar proteins. The hnRNP H protein family includes hnRNP H (also termed mcs94-1), hnRNP H2 (also termed FTP-3 or hnRNP H'), hnRNP F and hnRNP H3 (also termed hnRNP 2H9), which represent a group of nuclear RNA binding proteins that are involved in pre-mRNA processing. GRSF-1 is a cytoplasmic poly(A)+ mRNA binding protein which interacts with RNA in a G-rich element-dependent manner. It may function in RNA packaging, stabilization of RNA secondary structure, or other macromolecular interactions. ESRP1 (also termed RBM35A) and ESRP2 (also termed RBM35B) are epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of fibroblast growth factor receptor 2 (FGFR2), ENAH (also termed hMena), CD44 and CTNND1 (also termed p120-Catenin) transcripts. Fusilli shows high sequence homology to ESRPs. It can regulate endogenous FGFR2 splicing and functions as a splicing factor. The biological roles of both, RBM12 and RBM12B, remain unclear. RBM19 is a nucleolar protein conserved in eukaryotes. It is involved in ribosome biogenesis by processing rRNA. In addition, it is essential for preimplantation development. Members in this family contain 2~6 conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409699 [Multi-domain]  Cd Length: 73  Bit Score: 36.00  E-value: 5.15e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 304555603  65 LELQNVPRHASFSDVRRFLGRFGLQSHKIKLF----GQPPC-AFVTFRSAAERDKALR 117
Cdd:cd12254    2 VRLRGLPFSATEEDIRDFFSGLDIPPDGIHIVydddGRPTGeAYVEFASEEDAQRALR 59
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 97-137 8.35e-03

RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; This subfamily corresponds to the RRM1 of RBM28 and Nop4p. RBM28 is a specific nucleolar component of the spliceosomal small nuclear ribonucleoproteins (snRNPs), possibly coordinating their transition through the nucleolus. It specifically associates with U1, U2, U4, U5, and U6 small nuclear RNAs (snRNAs), and may play a role in the maturation of both small nuclear and ribosomal RNAs. RBM28 has four RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains), and an extremely acidic region between RRM2 and RRM3. The family also includes nucleolar protein 4 (Nop4p or Nop77p) encoded by YPL043W from Saccharomyces cerevisiae. It is an essential nucleolar protein involved in processing and maturation of 27S pre-rRNA and biogenesis of 60S ribosomal subunits. Nop4p also contains four RRMs.


Pssm-ID: 409847 [Multi-domain]  Cd Length: 79  Bit Score: 35.65  E-value: 8.35e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 304555603  97 GQPPC---AFVTFRSAAERDKALRVLHGALWKGCPLSVRLARPK 137
Cdd:cd12413   36 GKDKCrgfGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
RRM_SAFB_like cd12417
RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This ...
 64-131 9.84e-03

RNA recognition motif (RRM) found in the scaffold attachment factor (SAFB) family; This subfamily corresponds to the RRM domain of the SAFB family, including scaffold attachment factor B1 (SAFB1), scaffold attachment factor B2 (SAFB2), SAFB-like transcriptional modulator (SLTM), and similar proteins, which are ubiquitously expressed. SAFB1, SAFB2 and SLTM have been implicated in many diverse cellular processes including cell growth and transformation, stress response, and apoptosis. They share high sequence similarities and all contain a scaffold attachment factor-box (SAF-box, also known as SAP domain) DNA-binding motif, an RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), and a region rich in glutamine and arginine residues. SAFB1 is a nuclear protein with a distribution similar to that of SLTM, but unlike that of SAFB2, which is also found in the cytoplasm. To a large extent, SAFB1 and SLTM might share similar functions, such as the inhibition of an oestrogen reporter gene. The additional cytoplasmic localization of SAFB2 implies that it could play additional roles in the cytoplasmic compartment which are distinct from the nuclear functions shared with SAFB1 and SLTM.


Pssm-ID: 409851 [Multi-domain]  Cd Length: 74  Bit Score: 35.31  E-value: 9.84e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 304555603  64 KLELQNVPRHASFSDVRRFLGRFGL-QSHKI----KLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSV 131
Cdd:cd12417    1 NLWISGLSDTTKAADLKKIFSKYGKvVSAKVvtsaRTPGSRCYGYVTMASVEEADLCIKSLNKTELHGRVITV 73
 
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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