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Conserved domains on  [gi|124487423|ref|NP_001074468|]
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tRNA (uracil-5-)-methyltransferase homolog A isoform 2 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 168-577 1.34e-66

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: 221.97  E-value: 1.34e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 168 VPYTEQLEQKRLECERVLQKLAKEIGntnrallpwlllqrqqhnkacCPLEGVKPSPQQTEYRNKCEFlvgvGVDGKDNT 247
Cdd:COG2265   81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 248 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtssrgqamaiayfhpqk 326
Cdd:COG2265  136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 327 lsseevaglkaslvchfmegpgkasgvtslyfveegqrktpsqeglplehmAGDQCIQEDLLGLTFRISPHAFFQVNTPA 406
Cdd:COG2265  189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 407 AEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGL 486
Cdd:COG2265  218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLPEL 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 487 VSRLSSHqlVAVLDPPRAGLHSKVILAIRKAeNIKRLLYVSCNP----RaamgnfvDLCRAPSNRvkgtpFHPVKAVAVD 562
Cdd:COG2265  298 LWGGRPD--VVVLDPPRAGAGPEVLEALAAL-GPRRIVYVSCNPatlaR-------DLALLVEGG-----YRLEKVQPVD 362

                        410
                 ....*....|....*
gi 124487423 563 LFPQTPHCEMLILFE 577
Cdd:COG2265  363 MFPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 58-136 2.75e-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: 2.75e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487423  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 ...
 168-577 1.34e-66

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: 221.97  E-value: 1.34e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 168 VPYTEQLEQKRLECERVLQKLAKEIGntnrallpwlllqrqqhnkacCPLEGVKPSPQQTEYRNKCEFlvgvGVDGKDNT 247
Cdd:COG2265   81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 248 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtssrgqamaiayfhpqk 326
Cdd:COG2265  136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 327 lsseevaglkaslvchfmegpgkasgvtslyfveegqrktpsqeglplehmAGDQCIQEDLLGLTFRISPHAFFQVNTPA 406
Cdd:COG2265  189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 407 AEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGL 486
Cdd:COG2265  218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLPEL 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 487 VSRLSSHqlVAVLDPPRAGLHSKVILAIRKAeNIKRLLYVSCNP----RaamgnfvDLCRAPSNRvkgtpFHPVKAVAVD 562
Cdd:COG2265  298 LWGGRPD--VVVLDPPRAGAGPEVLEALAAL-GPRRIVYVSCNPatlaR-------DLALLVEGG-----YRLEKVQPVD 362

                        410
                 ....*....|....*
gi 124487423 563 LFPQTPHCEMLILFE 577
Cdd:COG2265  363 MFPHTHHVESVALLE 377
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 204-571 1.09e-39

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: 150.74  E-value: 1.09e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  204 LLQRQQHNKaccpLEGVKPSPQQTE----YRNKCEFLVGVGVDGKdntvgCRLGKYKGGT--------CAVAAPfdtvhi 271
Cdd:TIGR00479  88 LLERIGKFV----SEPIEDVPTIGDdpwgYRNKARLSLGRSPSGQ-----LQAGFYQKGShdivdvkqCPVQAP------ 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  272 peATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSSRGQAMAIAyFHPQKLSSEEVAGLKASLVCHFMEGPGKAS 351
Cdd:TIGR00479 153 --ALNALLPKVRAILENFGASRYLEHKELGQARHGVLRIGRHTGELSSV-DRTALERFPHKEELDLYLQPDSPDVKSICQ 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  352 GVTSlyfveegqRKTPSQEGLPLEHMAGDQCIQEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCC 431
Cdd:TIGR00479 230 NINP--------EKTNVIFGEETEVIAGEMPIYDKSGDLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYC 301

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  432 GTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGLVSRLSSHQLVaVLDPPRAGLHSKVI 511
Cdd:TIGR00479 302 GMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNGIANVTFYHGTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVL 380

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  512 LAIRKAENiKRLLYVSCNPRAAMGNFVDLCRAPSNRVKGTPfhpvkavaVDLFPQTPHCE 571
Cdd:TIGR00479 381 RTIIKLKP-ERIVYVSCNPATLARDLEALCKAGYTIARVQP--------VDMFPHTGHVE 431
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 58-136 2.75e-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: 2.75e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487423  58 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQSHKIKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLARP 136
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
375-578 2.56e-27

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


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 112.65  E-value: 2.56e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 375 EHMA---GDQCI--------QEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPK 443
Cdd:PRK03522 115 VHMAileGEEEIflteqqalPERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSMWDLFCGVGGFGLHCATP 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 444 VKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRA------EDLVPGLVsrlsshqlvaVLDPPRAGLhSKVILAIRKA 517
Cdd:PRK03522 195 GMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDStqfataQGEVPDLV----------LVNPPRRGI-GKELCDYLSQ 263

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487423 518 ENIKRLLYVSCNPrAAMGNfvDLCRAPSnrvkgtpFHPVKAVAVDLFPQTPHCEMLILFER 578
Cdd:PRK03522 264 MAPRFILYSSCNA-QTMAK--DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 398-578 2.44e-15

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 77.86  E-value: 2.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  398 AFFQVNTPAAEVLYtviqEWA-QLDGGST--VLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEF 474
Cdd:pfam05958 178 SFTQPNAAVNIKML----EWAcDVTQGSKgdLLELYCGNGNFSLALARNFRKVLATEIAKPSVAAAQYNIAANNIDNVQI 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  475 HCGRAEDLVPGLVS----------RLSSHQLVAVL-DPPRAGLHSKVILAIRKAENIkrlLYVSCNPRAAMGNFVDLcra 543
Cdd:pfam05958 254 IRMSAEEFTQAMNGvrefnrlkgiDLKSYNCSTIFvDPPRAGLDPETLKLVQAYPRI---LYISCNPETLCANLEQL--- 327

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 124487423  544 psnrvkgTPFHPVKAVAV-DLFPQTPHCEMLILFER 578
Cdd:pfam05958 328 -------SKTHRVERFALfDQFPYTHHMECGVLLEK 356
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 425-524 6.95e-12

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: 62.45  E-value: 6.95e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 425 TVLDVCCGTGTIGLALA-PKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGLVSRLSshqlVAVLDPPr 503
Cdd:cd02440    1 RVLDLGCGTGALALALAsGPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFD----VIISDPP- 75

                         90       100
                 ....*....|....*....|.
gi 124487423 504 agLHSKVILAIRKAENIKRLL 524
Cdd:cd02440   76 --LHHLVEDLARFLEEARRLL 94
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
69-139 2.28e-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: 2.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  69 NVPRHASFSDVRRFLGRFGL-QSHKI---------KLFGqppcaFVTFRSAAERDKALRVLHGALWKGCPLSVRLARPKA 138
Cdd:COG0724    8 NLPYSVTEEDLRELFSEYGEvTSVKLitdretgrsRGFG-----FVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82


                 .
gi 124487423 139 D 139
Cdd:COG0724   83 E 83
RRM smart00360
RNA recognition motif;
69-131 1.49e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 1.49e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124487423    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 ...
 168-577 1.34e-66

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: 221.97  E-value: 1.34e-66
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 168 VPYTEQLEQKRLECERVLQKLAKEIGntnrallpwlllqrqqhnkacCPLEGVKPSPQQTEYRNKCEFlvgvGVDGKDNT 247
Cdd:COG2265   81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 248 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtssrgqamaiayfhpqk 326
Cdd:COG2265  136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 327 lsseevaglkaslvchfmegpgkasgvtslyfveegqrktpsqeglplehmAGDQCIQEDLLGLTFRISPHAFFQVNTPA 406
Cdd:COG2265  189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                        250       260       270       280       290       300       310       320
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 407 AEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGL 486
Cdd:COG2265  218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLARRAKKVIGVEIVPEAVEDARENARLNGLKNVEFVAGDLEEVLPEL 297

                        330       340       350       360       370       380       390       400
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 487 VSRLSSHqlVAVLDPPRAGLHSKVILAIRKAeNIKRLLYVSCNP----RaamgnfvDLCRAPSNRvkgtpFHPVKAVAVD 562
Cdd:COG2265  298 LWGGRPD--VVVLDPPRAGAGPEVLEALAAL-GPRRIVYVSCNPatlaR-------DLALLVEGG-----YRLEKVQPVD 362

                        410
                 ....*....|....*
gi 124487423 563 LFPQTPHCEMLILFE 577
Cdd:COG2265  363 MFPHTHHVESVALLE 377
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 204-571 1.09e-39

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: 150.74  E-value: 1.09e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  204 LLQRQQHNKaccpLEGVKPSPQQTE----YRNKCEFLVGVGVDGKdntvgCRLGKYKGGT--------CAVAAPfdtvhi 271
Cdd:TIGR00479  88 LLERIGKFV----SEPIEDVPTIGDdpwgYRNKARLSLGRSPSGQ-----LQAGFYQKGShdivdvkqCPVQAP------ 152

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  272 peATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSSRGQAMAIAyFHPQKLSSEEVAGLKASLVCHFMEGPGKAS 351
Cdd:TIGR00479 153 --ALNALLPKVRAILENFGASRYLEHKELGQARHGVLRIGRHTGELSSV-DRTALERFPHKEELDLYLQPDSPDVKSICQ 229

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  352 GVTSlyfveegqRKTPSQEGLPLEHMAGDQCIQEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCC 431
Cdd:TIGR00479 230 NINP--------EKTNVIFGEETEVIAGEMPIYDKSGDLSFTFSARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYC 301

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  432 GTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGLVSRLSSHQLVaVLDPPRAGLHSKVI 511
Cdd:TIGR00479 302 GMGTFTLPLAKQAKSVVGVEGVPESVEKAQQNAELNGIANVTFYHGTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVL 380

                         330       340       350       360       370       380
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  512 LAIRKAENiKRLLYVSCNPRAAMGNFVDLCRAPSNRVKGTPfhpvkavaVDLFPQTPHCE 571
Cdd:TIGR00479 381 RTIIKLKP-ERIVYVSCNPATLARDLEALCKAGYTIARVQP--------VDMFPHTGHVE 431
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 58-136 2.75e-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: 2.75e-39
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487423  58 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQSHKIKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLARP 136
Cdd:cd12439    1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
375-578 2.56e-27

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


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 112.65  E-value: 2.56e-27
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 375 EHMA---GDQCI--------QEDLLGLTFRISPHAFFQVNTPAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPK 443
Cdd:PRK03522 115 VHMAileGEEEIflteqqalPERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWVRELPPRSMWDLFCGVGGFGLHCATP 194

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 444 VKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRA------EDLVPGLVsrlsshqlvaVLDPPRAGLhSKVILAIRKA 517
Cdd:PRK03522 195 GMQLTGIEISAEAIACAKQSAAELGLTNVQFQALDStqfataQGEVPDLV----------LVNPPRRGI-GKELCDYLSQ 263

                        170       180       190       200       210       220
                 ....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487423 518 ENIKRLLYVSCNPrAAMGNfvDLCRAPSnrvkgtpFHPVKAVAVDLFPQTPHCEMLILFER 578
Cdd:PRK03522 264 MAPRFILYSSCNA-QTMAK--DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
389-578 1.23e-22

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


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 101.00  E-value: 1.23e-22
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 389 GLTFRISPHAFFQVNTPAAEVLytVIQ--EWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALT 466
Cdd:PRK13168 264 GLRLAFSPRDFIQVNAQVNQKM--VARalEWLDPQPGDRVLDLFCGLGNFTLPLARQAAEVVGVEGVEAMVERARENARR 341

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 467 NELSNVEFHCgraEDLvpglvSRLSSHQLVAV-------LDPPRAGLhSKVILAIRKAeNIKRLLYVSCNPraamgnfVD 539
Cdd:PRK13168 342 NGLDNVTFYH---ANL-----EEDFTDQPWALggfdkvlLDPPRAGA-AEVMQALAKL-GPKRIVYVSCNP-------AT 404

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 124487423 540 LCRAPSNRVKGtPFHPVKAVAVDLFPQTPHCEMLILFER 578
Cdd:PRK13168 405 LARDAGVLVEA-GYRLKRAGMLDMFPHTGHVESMALFER 442
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 398-578 2.44e-15

tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC:2.1.1.35 from bacteria, archaea and eukaryotes. A 5-methyluridine (m(5)U) residue at position 54 is a conserved feature of bacterial and eukaryotic tRNAs. The methylation of U54 is catalyzed by the tRNA(m5U54)methyltransferase, which in Saccharomyces cerevisiae is encoded by the nonessential TRM2 gene. It is thought that tRNA modification enzymes might have a role in tRNA maturation not necessarily linked to their known catalytic activity.


Pssm-ID: 428692  Cd Length: 357  Bit Score: 77.86  E-value: 2.44e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  398 AFFQVNTPAAEVLYtviqEWA-QLDGGST--VLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEF 474
Cdd:pfam05958 178 SFTQPNAAVNIKML----EWAcDVTQGSKgdLLELYCGNGNFSLALARNFRKVLATEIAKPSVAAAQYNIAANNIDNVQI 253

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  475 HCGRAEDLVPGLVS----------RLSSHQLVAVL-DPPRAGLHSKVILAIRKAENIkrlLYVSCNPRAAMGNFVDLcra 543
Cdd:pfam05958 254 IRMSAEEFTQAMNGvrefnrlkgiDLKSYNCSTIFvDPPRAGLDPETLKLVQAYPRI---LYISCNPETLCANLEQL--- 327

                         170       180       190
                  ....*....|....*....|....*....|....*.
gi 124487423  544 psnrvkgTPFHPVKAVAV-DLFPQTPHCEMLILFER 578
Cdd:pfam05958 328 -------SKTHRVERFALfDQFPYTHHMECGVLLEK 356
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
 390-578 1.33e-14

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 75.64  E-value: 1.33e-14
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 390 LTFRISPHAFFQVNTpaaevlyTVIQ---EWAQ---LDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMN 463
Cdd:PRK05031 175 FIYRQVENSFTQPNA-------AVNEkmlEWALdatKGSKGDLLELYCGNGNFTLALARNFRRVLATEISKPSVAAAQYN 247

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 464 ALTNELSNVEFHCGRAEDLVPGLVSR----------LSSHQLVAVL-DPPRAGLHSKVILAIRKAENIkrlLYVSCNPRA 532
Cdd:PRK05031 248 IAANGIDNVQIIRMSAEEFTQAMNGVrefnrlkgidLKSYNFSTIFvDPPRAGLDDETLKLVQAYERI---LYISCNPET 324

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*..
gi 124487423 533 AMGNFVDLCRApsnrvkgtpfHPVKAVAV-DLFPQTPHCEMLILFER 578
Cdd:PRK05031 325 LCENLETLSQT----------HKVERFALfDQFPYTHHMECGVLLEK 361
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 426-482 2.39e-12

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 63.35  E-value: 2.39e-12
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*...
gi 124487423  426 VLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDARMNALTNELsNVEFHCGRAEDL 482
Cdd:pfam13649   1 VLDLGCGTGRLTLALARRGGaRVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAEDL 57
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 416-482 5.50e-12

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: 63.47  E-value: 5.50e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124487423 416 EWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELsNVEFHCGRAEDL 482
Cdd:COG2226   16 AALGLRPGARVLDLGCGTGRLALALAERGARVTGVDISPEMLELARERAAEAGL-NVEFVVGDAEDL 81
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 425-524 6.95e-12

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: 62.45  E-value: 6.95e-12
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 425 TVLDVCCGTGTIGLALA-PKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGLVSRLSshqlVAVLDPPr 503
Cdd:cd02440    1 RVLDLGCGTGALALALAsGPGARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEADESFD----VIISDPP- 75

                         90       100
                 ....*....|....*....|.
gi 124487423 504 agLHSKVILAIRKAENIKRLL 524
Cdd:cd02440   76 --LHHLVEDLARFLEEARRLL 94
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 369-477 1.54e-11

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


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 65.17  E-value: 1.54e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 369 QEGLPLEHMAGdqciQEDLLGLTFRISPHAFfqV---NTpaaEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALA---P 442
Cdd:COG2890   65 AAGEPLAYILG----EAEFYGLEFKVDPGVL--IprpET---EELVELALALLPAGAPPRVLDLGTGSGAIALALAkerP 135

                         90       100       110
                 ....*....|....*....|....*....|....*.
gi 124487423 443 KVkRVVGIELCQEAVEDARMNALTNELSN-VEFHCG 477
Cdd:COG2890  136 DA-RVTAVDISPDALAVARRNAERLGLEDrVRFLQG 170
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 405-484 1.71e-11

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


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 63.78  E-value: 1.71e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 405 PAAEVLYTVIQEwaqLDGGSTVLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLV 483
Cdd:COG0500   12 PGLAALLALLER---LPKGGRVLDLGCGTGRNLLALAARFGgRVIGIDLSPEAIALARARAAKAGLGNVEFLVADLAELD 88


                 .
gi 124487423 484 P 484
Cdd:COG0500   89 P 89
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 417-477 2.99e-11

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: 63.63  E-value: 2.99e-11
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124487423 417 WAQLDGGSTVLDVCCGTGTIGLALAPKVK--RVVGIELCQEAVEDARMNALTNELSN-VEFHCG 477
Cdd:COG4123   32 FAPVKKGGRVLDLGTGTGVIALMLAQRSPgaRITGVEIQPEAAELARRNVALNGLEDrITVIHG 95
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 370-477 3.38e-11

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


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 64.03  E-value: 3.38e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 370 EGLPLEHMAGdqciQEDLLGLTFRISPHAFfqVNTPAAEVLytViqEWA----QLDGGSTVLDVCCGTGTIGLALA---P 442
Cdd:PRK09328  62 AGEPLQYILG----EAEFWGLDFKVSPGVL--IPRPETEEL--V--EWAlealLLKEPLRVLDLGTGSGAIALALAkerP 131

                         90       100       110
                 ....*....|....*....|....*....|....*
gi 124487423 443 KVkRVVGIELCQEAVEDARMNALTNELSNVEFHCG 477
Cdd:PRK09328 132 DA-EVTAVDISPEALAVARRNAKHGLGARVEFLQG 165
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 420-482 6.08e-11

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 60.89  E-value: 6.08e-11
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124487423  420 LDGGSTVLDVCCGTGTIGLALAPKV---KRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDL 482
Cdd:pfam13847   1 IDKGMRVLDLGCGTGHLSFELAEELgpnAEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDIEEL 66
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 410-482 1.37e-10

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: 59.26  E-value: 1.37e-10
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124487423 410 LYTVIQEWaqLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNAltnELSNVEFHCGRAEDL 482
Cdd:COG2227   14 LAALLARL--LPAGGRVLDVGCGTGRLALALARRGADVTGVDISPEALEIARERA---AELNVDFVQGDLEDL 81
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
422-485 4.04e-09

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 54.06  E-value: 4.04e-09
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124487423 422 GGSTVLDVCCGTGTIGLALAPKVK--RVVGIELCQEAVEDARMNaltneLSNVEFHCGRAEDLVPG 485
Cdd:COG4106    1 PPRRVLDLGCGTGRLTALLAERFPgaRVTGVDLSPEMLARARAR-----LPNVRFVVADLRDLDPP 61
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
406-482 4.44e-09

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


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 56.16  E-value: 4.44e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124487423 406 AAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALtnelsNVEFHCGRAEDL 482
Cdd:COG4976   30 APALLAEELLARLPPGPFGRVLDLGCGTGLLGEALRPRGYRLTGVDLSEEMLAKAREKGV-----YDRLLVADLADL 101
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 417-475 6.75e-09

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: 55.97  E-value: 6.75e-09
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 124487423 417 WAQLDGGS-------------TVLDVCCGTGTIGLALA--PKVKRVVGIELCQEAVEDARMNALTNELSNVEFH 475
Cdd:COG2813   31 RDRLDIGTrlllehlpeplggRVLDLGCGYGVIGLALAkrNPEARVTLVDVNARAVELARANAAANGLENVEVL 104
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
401-521 1.08e-08

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 55.30  E-value: 1.08e-08
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 401 QVNTP---AAEVLYTviqewAQLDG---GSTVLDVCCGTGTIGLALAPK-VKRVVGIELCQEAVEDARMNALtNELSNVE 473
Cdd:COG2263   23 QYPTPaelAAELLHL-----AYLRGdieGKTVLDLGCGTGMLAIGAALLgAKKVVGVDIDPEALEIARENAE-RLGVRVD 96

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 124487423 474 FHCGRAEDLvpglvsRLSSHQLVAVLDPP--------------RAGLHSKVILAIRKAENIK 521
Cdd:COG2263   97 FIRADVTRI------PLGGSVDTVVMNPPfgaqrrhadrpfleKALEIAAVIYSIHNAGSLD 152
PCMT pfam01135
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);
416-477 2.76e-07

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


Pssm-ID: 395902 [Multi-domain]  Cd Length: 205  Bit Score: 51.60  E-value: 2.76e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124487423  416 EWAQLDGGSTVLDVCCGTGTIGLALAPKVK---RVVGIELCQEAVEDARMNALTNELSNVEFHCG 477
Cdd:pfam01135  67 ELLELKPGMRVLEIGSGSGYLTACFARMVGevgRVVSIEHIPELVEIARRNLEKLGLENVIVVVG 131
PRK08317 PRK08317
hypothetical protein; Provisional
 404-482 5.52e-07

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 51.09  E-value: 5.52e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 404 TPAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVK---RVVGIELCQEAVEDARMNAlTNELSNVEFHCGRAE 480
Cdd:PRK08317   1 LPDFRRYRARTFELLAVQPGDRVLDVGCGPGNDARELARRVGpegRVVGIDRSEAMLALAKERA-AGLGPNVEFVRGDAD 79


                 ..
gi 124487423 481 DL 482
Cdd:PRK08317  80 GL 81
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 416-482 6.84e-07

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: 50.72  E-value: 6.84e-07
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  416 EWAQLDGGSTVLDVCCGTGTIGLALA---PKVKRVVGIELCQEAVEDARMNALTNElsNVEFHCGRAEDL 482
Cdd:TIGR01934  33 KLIGVFKGQKVLDVACGTGDLAIELAksaPDRGKVTGVDFSSEMLEVAKKKSELPL--NIEFIQADAEAL 100
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 405-484 7.12e-07

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


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 49.16  E-value: 7.12e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 405 PAAEVLYTVIQEWAQLDGGSTVLDVCCGTGTIGLALAPKVK-RVVGIELCQEAVEDARMNALTNELSN-VEFHCGRAEDL 482
Cdd:COG2230   34 EAQEAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLARRYGvRVTGVTLSPEQLEYARERAAEAGLADrVEVRLADYRDL 113


                 ..
gi 124487423 483 VP 484
Cdd:COG2230  114 PA 115
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 69-132 8.87e-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: 8.87e-07
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124487423  69 NVPRHASFSDVRRFLGRFG-LQSHKI---KLFGQPPCAFVTFRSAAERDKALRVLHGALWKGCPLSVR 132
Cdd:cd00590    5 NLPPDTTEEDLRELFSKFGeVVSVRIvrdRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 418-502 1.28e-06

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: 48.79  E-value: 1.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 418 AQLDGGSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLvpglvsRLSSHQL-V 496
Cdd:COG1041   22 AGAKEGDTVLDPFCGTGTILIEAGLLGRRVIGSDIDPKMVEGARENLEHYGYEDADVIRGDARDL------PLADESVdA 95


                 ....*.
gi 124487423 497 AVLDPP 502
Cdd:COG1041   96 IVTDPP 101
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 69-131 1.98e-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: 45.70  E-value: 1.98e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124487423  69 NVPRHASFSDVRRFLGRFGLQShkIKLFGQPP----CAFVTFRSAAERDKALRVLHGALWKGCPLSV 131
Cdd:cd12238    6 HLPPELSEDDKEDLLKHFGATS--VRVMKRRGklkhTAFATFDNEQAASKALSRLHQLKILGKRLVV 70
PRK14968 PRK14968
putative methyltransferase; Provisional
 423-474 2.11e-06

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 48.36  E-value: 2.11e-06
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....
gi 124487423 423 GSTVLDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNALTNELSN--VEF 474
Cdd:PRK14968  24 GDRVLEVGTGSGIVAIVAAKNGKKVVGVDINPYAVECAKCNAKLNNIRNngVEV 77
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
69-139 2.28e-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: 2.28e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  69 NVPRHASFSDVRRFLGRFGL-QSHKI---------KLFGqppcaFVTFRSAAERDKALRVLHGALWKGCPLSVRLARPKA 138
Cdd:COG0724    8 NLPYSVTEEDLRELFSEYGEvTSVKLitdretgrsRGFG-----FVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPRE 82


                 .
gi 124487423 139 D 139
Cdd:COG0724   83 E 83
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 427-482 3.58e-06

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


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 45.73  E-value: 3.58e-06
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 124487423  427 LDVCCGTGTIGLALAPKVKRVVGIELCQEAVEDARMNAltnELSNVEFHCGRAEDL 482
Cdd:pfam08241   1 LDVGCGTGLLTELLARLGARVTGVDISPEMLELAREKA---PREGLTFVVGDAEDL 53
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 416-482 6.44e-06

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


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 47.84  E-value: 6.44e-06
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487423 416 EWAQLDGGSTVLDVCCGTGTIGLALA---PKVKRVVGIELCQEAVEDARMNALTNELS-NVEFHCGRAEDL 482
Cdd:PRK00216  45 KWLGVRPGDKVLDLACGTGDLAIALAkavGKTGEVVGLDFSEGMLAVGREKLRDLGLSgNVEFVQGDAEAL 115
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 369-502 1.01e-05

23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure and biogenesis]; 23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI is part of the Pathway/BioSystem: 23S rRNA modification


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 48.25  E-value: 1.01e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 369 QEGLPLE--HMAGDQC----IQEDllGLTFRISPHA-----FF--QVNTPAAevlytvIQEWAQldgGSTVLDVCCGTGT 435
Cdd:COG1092  161 LEGLPQYegVLYGEAPeeveVEEN--GLKFLVDLTDgqktgLFldQRENRAR------VAELAK---GKRVLNLFSYTGG 229

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487423 436 IGL-ALAPKVKRVVGIELCQEAVEDARMNALTNELS-NVEFHCGRAEDLVPGLVSRLSSHQLVaVLDPP 502
Cdd:COG1092  230 FSVhAAAGGAKSVTSVDLSATALEWAKENAALNGLDdRHEFVQADAFDWLRELAREGERFDLI-ILDPP 297
hemK_fam TIGR00536
HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme ...
 370-486 3.91e-05

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: 45.81  E-value: 3.91e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  370 EGLPLEHMAGdqciQEDLLGLTFRISPHaffqVNTPAAEVLYTVIQEWAQL---DGGSTVLDVCCGTGTIGLALAPKV-- 444
Cdd:TIGR00536  67 KGVPVAYLLG----SKEFYGLEFFVNEH----VLIPRPETEELVEKALASLisqPPILHILDLGTGSGCIALALAYEFpn 138

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 124487423  445 KRVVGIELCQEAVEDARMNALTNELS-NVEFHCGRAEDLVPGL 486
Cdd:TIGR00536 139 AEVIAVDISPDALAVAEENAEKNQLEhRVEFIQSNLFEPLAGQ 181
CobL COG2242
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part ...
 423-486 5.66e-05

Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part of the Pathway/BioSystem: Cobalamine/B12 biosynthesis


Pssm-ID: 441843 [Multi-domain]  Cd Length: 403  Bit Score: 45.93  E-value: 5.66e-05
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 124487423 423 GSTVLDVCCGTGTIGL--ALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLVPGL 486
Cdd:COG2242  248 GDVLWDIGAGSGSVSIeaARLAPGGRVYAIERDPERAALIRANARRFGVPNVEVVEGEAPEALADL 313
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 417-475 1.21e-04

Methyltransferase small domain; This domain is found in ribosomal RNA small subunit methyltransferase C as well as other methyltransferases.


Pssm-ID: 428349 [Multi-domain]  Cd Length: 170  Bit Score: 42.96  E-value: 1.21e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 124487423  417 WAQLDGGS-------------TVLDVCCGTGTIGLALA---PKVKrVVGIELCQEAVEDARMNALTNELSNVEFH 475
Cdd:pfam05175  13 HGRLDIGSrlllehlpkdlsgKVLDLGCGAGVLGAALAkesPDAE-LTMVDINARALESARENLAANGLENGEVV 86
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 64-134 1.36e-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: 1.36e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  64 KLELQNVPRHASFSDVRRFLGRFgLQSHK-------IKLF------GQppcAFVTFRSAAERDKALRVLHGALWKGCPLS 130
Cdd:cd12239    3 RLYVKNLSKRVSEKDLKYIFGRF-VDSSSeeknmfdIRLMtegrmkGQ---AFITFPSEELAEKALNLTNGYVLHGKPMV 78


                 ....
gi 124487423 131 VRLA 134
Cdd:cd12239   79 VQFA 82
RRM smart00360
RNA recognition motif;
69-131 1.49e-04

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 40.27  E-value: 1.49e-04
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 124487423    69 NVPRHASFSDVRRFLGRFG----LQSHKIKLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGCPLSV 131
Cdd:smart00360   6 NLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSkGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
arsM PRK11873
arsenite methyltransferase;
415-482 2.19e-04

arsenite methyltransferase;


Pssm-ID: 237007 [Multi-domain]  Cd Length: 272  Bit Score: 43.40  E-value: 2.19e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 124487423 415 QEWAQLDGGSTVLDVCCGTGTIGLALAPKV---KRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDL 482
Cdd:PRK11873  70 TALAELKPGETVLDLGSGGGFDCFLAARRVgptGKVIGVDMTPEMLAKARANARKAGYTNVEFRLGEIEAL 140
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 423-518 2.34e-04

16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA G966 N2-methylase RsmD is part of the Pathway/BioSystem: 16S rRNA modification


Pssm-ID: 440505 [Multi-domain]  Cd Length: 183  Bit Score: 42.38  E-value: 2.34e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 423 GSTVLDVCCGTGTIGL-AL---ApkvKRVVGIELCQEAVEDARMNA-LTNELSNVEFHCGRAEDLVPGLVSRlsSHQLVa 497
Cdd:COG0742   42 GARVLDLFAGSGALGLeALsrgA---ASVVFVEKDRKAAAVIRKNLeKLGLEDRARVIRGDALRFLKRLAGE--PFDLV- 115

                         90       100
                 ....*....|....*....|..
gi 124487423 498 VLDPP-RAGLHSKVILAIRKAE 518
Cdd:COG0742  116 FLDPPyAKGLLEKALELLAENG 137
Ubie_methyltran pfam01209
ubiE/COQ5 methyltransferase family;
423-482 2.48e-04

ubiE/COQ5 methyltransferase family;


Pssm-ID: 395966 [Multi-domain]  Cd Length: 228  Bit Score: 42.81  E-value: 2.48e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 124487423  423 GSTVLDVCCGTGTIGLALAPKVK---RVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDL 482
Cdd:pfam01209  43 GNKFLDVAGGTGDWTFGLSDSAGssgKVVGLDINENMLKEGEKKAKEEGKYNIEFLQGNAEEL 105
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
417-516 4.00e-04

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 41.46  E-value: 4.00e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  417 WAQLDGGSTVLDVCCGTGTIGL-ALAPKVKRVVGIELCQEAVEDARMNALTNELSNVEFHCGRAEDLvPGLVSRLSSHQL 495
Cdd:pfam03602  36 LAPYIEGARVLDLFAGSGALGLeALSRGAKRVTLVEKDKRAVQILKENLQLLGLPGAVLVMDALLAL-LRLAGKGPVFDI 114

                          90       100
                  ....*....|....*....|..
gi 124487423  496 VaVLDPP-RAGLHSKVILAIRK 516
Cdd:pfam03602 115 V-FLDPPyAKGLIEEVLDLLAE 135
PrmA COG2264
Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];
416-483 4.72e-04

Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];


Pssm-ID: 441865 [Multi-domain]  Cd Length: 284  Bit Score: 42.47  E-value: 4.72e-04
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 124487423 416 EW--AQLDGGSTVLDVCCGTGtIgLALAPK---VKRVVGIELCQEAVEDARMNALTNELSN-VEFHCGRAE-----DLV 483
Cdd:COG2264  140 EAleKLLKPGKTVLDVGCGSG-I-LAIAAAklgAKRVLAVDIDPVAVEAARENAELNGVEDrIEVVLGDLLedgpyDLV 216
PRK14967 PRK14967
putative methyltransferase; Provisional
 420-465 4.94e-04

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 41.96  E-value: 4.94e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124487423 420 LDGGSTVLDVCCGTGTIGLALAPK-VKRVVGIELCQEAVEDARMNAL 465
Cdd:PRK14967  34 LGPGRRVLDLCTGSGALAVAAAAAgAGSVTAVDISRRAVRSARLNAL 80
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 91-135 1.01e-03

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: 1.01e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 124487423  91 HKI-KLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGCPLSVRLAR 135
Cdd:cd12355   34 HKTgPLKGQPrGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWAH 80
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 1.03e-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: 1.03e-03
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 124487423  64 KLELQNVPRHASFSDVRRFLGRFG----LQSHKIKLFGQPP-CAFVTFRSAAERDKALRVLHGA-LWKGC--PLSVR 132
Cdd:cd12361    1 KLFVGMIPKTASEEDVRPLFEQFGnieeVQILRDKQTGQSKgCAFVTFSTREEALRAIEALHNKkTMPGCssPLQVK 77
COG2521 COG2521
Predicted archaeal methyltransferase [General function prediction only];
423-506 1.78e-03

Predicted archaeal methyltransferase [General function prediction only];


Pssm-ID: 442011 [Multi-domain]  Cd Length: 285  Bit Score: 40.66  E-value: 1.78e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423 423 GSTVLDVCCGTG--TIGlALAPKVKRVVGIELCQEAVEDARMNALTNELSN--VEFHCGRAEDLVPglvsRLSSHQLVAV 498
Cdd:COG2521  133 GDRVLDTCTGLGytAIE-ALKRGAREVITVEKDPNVLELAELNPWSRELANerIKIILGDASEVIK----TFPDESFDAI 207


                 ....*....
gi 124487423 499 L-DPPRAGL 506
Cdd:COG2521  208 IhDPPRFSL 216
RRM_NELFE cd12305
RNA recognition motif in negative elongation factor E (NELF-E) and similar proteins; This ...
 101-135 1.83e-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: 1.83e-03
                         10        20        30
                 ....*....|....*....|....*....|....*
gi 124487423 101 CAFVTFRSAAERDKALRVLHGALWKGCPLSVRLAR 135
Cdd:cd12305   40 CAFVTFEKMESADQAIAELNGTTVEGVQLKVSIAR 74
PrmA pfam06325
Ribosomal protein L11 methyltransferase (PrmA); This family consists of several Ribosomal ...
 416-471 2.25e-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: 40.33  E-value: 2.25e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  416 EW--AQLDGGSTVLDVCCGTGTIGLAlAPK--VKRVVGIELCQEAVEDARMNALTNELSN 471
Cdd:pfam06325 153 EAleRLVKPGESVLDVGCGSGILAIA-ALKlgAKKVVGVDIDPVAVRAAKENAELNGVEA 211
RRM_SR140 cd12223
RNA recognition motif (RRM) found in U2-associated protein SR140 and similar proteins; This ...
 59-136 2.70e-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: 2.70e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 124487423  59 TSEIFkleLQNVPRHASFSDVRRFLGRFG-LQSHKIkLFGQPP--------CAFVTFRSAAERDKALRVLHGALWKGCPL 129
Cdd:cd12223    1 TTNLY---VGNLPPSVTEEVLLREFGRFGpLASVKI-MWPRTEeerrrnrnCGFVAFMSRADAERAMRELNGKDVMGYEL 76


                 ....*..
gi 124487423 130 SVRLARP 136
Cdd:cd12223   77 KLGWGKA 83
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 65-117 5.51e-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: 5.51e-03
                         10        20        30        40        50
                 ....*....|....*....|....*....|....*....|....*....|....*...
gi 124487423  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 8.27e-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: 8.27e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....
gi 124487423  97 GQPPC---AFVTFRSAAERDKALRVLHGALWKGCPLSVRLARPK 137
Cdd:cd12413   36 GKDKCrgfGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
 
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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