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Conserved domains on  [gi|1061899871|ref|NP_001317968|]
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tRNA (uracil-5-)-methyltransferase homolog A isoform c [Homo sapiens]

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 ...
 178-605 6.64e-64

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: 215.43  E-value: 6.64e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 178 VPYAEQLERKQLECEQVLQKLAKEIGstnrallpwlleqrhkhnkacCPLEGVRPSPQQTEYRNKCEFlvgvGVDGEDNT 257
Cdd:COG2265    81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 258 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtsrrhqamaiayfhpqk 336
Cdd:COG2265   136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 337 lspeelaelktslaqhftagpgrasgvtclyfveegqrktpsqeglplehvAGDRCIHEDLLGLTFRISPHAFFQVNTPA 416
Cdd:COG2265   189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 417 AEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNE 496
Cdd:COG2265   218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLAR------------------RAKKVIGVEIVPEAVEDARENARLNG 279

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 497 LSNVEFHCGRAEDLVPTLVSRLASQhlVAILDPPRAGLHSKVILAIRRAKnLRRLLYVSCNP----RaamgnfvDLCRAP 572
Cdd:COG2265   280 LKNVEFVAGDLEEVLPELLWGGRPD--VVVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPatlaR-------DLALLV 349

                         410       420       430
                  ....*....|....*....|....*....|...
gi 1061899871 573 SNRvkgipFRPVKAVAVDLFPQTPHCEMLILFE 605
Cdd:COG2265   350 EGG-----YRLEKVQPVDMFPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 68-146 4.69e-40

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: 140.84  E-value: 4.69e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1061899871  68 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQPHKTKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGRPLSVRLARP 146
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 ...
 178-605 6.64e-64

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: 215.43  E-value: 6.64e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 178 VPYAEQLERKQLECEQVLQKLAKEIGstnrallpwlleqrhkhnkacCPLEGVRPSPQQTEYRNKCEFlvgvGVDGEDNT 257
Cdd:COG2265    81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 258 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtsrrhqamaiayfhpqk 336
Cdd:COG2265   136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 337 lspeelaelktslaqhftagpgrasgvtclyfveegqrktpsqeglplehvAGDRCIHEDLLGLTFRISPHAFFQVNTPA 416
Cdd:COG2265   189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 417 AEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNE 496
Cdd:COG2265   218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLAR------------------RAKKVIGVEIVPEAVEDARENARLNG 279

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 497 LSNVEFHCGRAEDLVPTLVSRLASQhlVAILDPPRAGLHSKVILAIRRAKnLRRLLYVSCNP----RaamgnfvDLCRAP 572
Cdd:COG2265   280 LKNVEFVAGDLEEVLPELLWGGRPD--VVVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPatlaR-------DLALLV 349

                         410       420       430
                  ....*....|....*....|....*....|...
gi 1061899871 573 SNRvkgipFRPVKAVAVDLFPQTPHCEMLILFE 605
Cdd:COG2265   350 EGG-----YRLEKVQPVDMFPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 68-146 4.69e-40

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: 140.84  E-value: 4.69e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1061899871  68 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQPHKTKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGRPLSVRLARP 146
Cdd:cd12439     1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 178-599 5.51e-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: 149.20  E-value: 5.51e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 178 VPYAEQLERKQLECEQVLQklakeigstnrallpwlleqRHKHNKaccpLEGVRPSPQQTE----YRNKCEFLVGvgvdg 253
Cdd:TIGR00479  72 LSYELQLRSKQQQVIALLE--------------------RIGKFV----SEPIEDVPTIGDdpwgYRNKARLSLG----- 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 254 EDNTVGCRLGKYKGGT--------CAVAAPfdtvhipeATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSRRHQ 325
Cdd:TIGR00479 123 RSPSGQLQAGFYQKGShdivdvkqCPVQAP--------ALNALLPKVRAILENFGASRYLEHKELGQARHGVLRIGRHTG 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 326 AMAIAyFHPQKLSPEELAELKTSLAQHFTAGPGRASGVTclyfveegQRKTPSQEGLPLEHVAGDRCIHEDLLGLTFRIS 405
Cdd:TIGR00479 195 ELSSV-DRTALERFPHKEELDLYLQPDSPDVKSICQNIN--------PEKTNVIFGEETEVIAGEMPIYDKSGDLSFTFS 265

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 406 PHAFFQVNTPAAEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARGpmysppwvgrhhaflfqkVKRVIGVELCPEAV 485
Cdd:TIGR00479 266 ARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQ------------------AKSVVGVEGVPESV 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 486 EDARVNAQDNELSNVEFHCGRAEDLVPTLVSRLASQHLVaILDPPRAGLHSKVILAIRRAKNlRRLLYVSCNPRAAMGNF 565
Cdd:TIGR00479 328 EKAQQNAELNGIANVTFYHGTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVLRTIIKLKP-ERIVYVSCNPATLARDL 405

                         410       420       430
                  ....*....|....*....|....*....|....
gi 1061899871 566 VDLCRApsnrvkgiPFRPVKAVAVDLFPQTPHCE 599
Cdd:TIGR00479 406 EALCKA--------GYTIARVQPVDMFPHTGHVE 431
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
385-606 7.40e-24

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


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 102.64  E-value: 7.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 385 EHVA---GDRCIH--------EDLLGLTFRISPHAFFQVNTPAAEVLYTVIQDW-AQLDAGSMVlDVCCGTGTIGLALAR 452
Cdd:PRK03522  115 VHMAileGEEEIFlteqqalpERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWvRELPPRSMW-DLFCGVGGFGLHCAT 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 453 GPMysppwvgrhhaflfqkvkRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRA------EDLVPTLVsrlasqhlvaI 526
Cdd:PRK03522  194 PGM------------------QLTGIEISAEAIACAKQSAAELGLTNVQFQALDStqfataQGEVPDLV----------L 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 527 LDPPRAGLhSKVILAIRRAKNLRRLLYVSCNPrAAMGNfvDLCRAPSnrvkgipFRPVKAVAVDLFPQTPHCEMLILFER 606
Cdd:PRK03522  246 VNPPRRGI-GKELCDYLSQMAPRFILYSSCNA-QTMAK--DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 436-556 3.15e-11

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: 60.52  E-value: 3.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 436 VLDVCCGTGTIGLALARGPmysppwvgrhhaflfqkVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRAEDLVPTLV 515
Cdd:cd02440     2 VLDLGCGTGALALALASGP-----------------GARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEAD 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1061899871 516 SRLAsqhlVAILDPP---RAGLHSKVILAIRRAKNLRRLLYVSC 556
Cdd:cd02440    65 ESFD----VIISDPPlhhLVEDLARFLEEARRLLKPGGVLVLTL 104
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 436-510 5.90e-11

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 59.11  E-value: 5.90e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1061899871 436 VLDVCCGTGTIGLALARgpmysppwvgRHHAflfqkvkRVIGVELCPEAVEDARVNAQDNELsNVEFHCGRAEDL 510
Cdd:pfam13649   1 VLDLGCGTGRLTLALAR----------RGGA-------RVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAEDL 57
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
112-149 1.24e-07

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 49.33  E-value: 1.24e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1061899871 112 AFVTFRSAAERDKALRVLHGALWKGRPLSVRLARPKAD 149
Cdd:COG0724    46 GFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83
RRM smart00360
RNA recognition motif;
79-141 5.28e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.51  E-value: 5.28e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1061899871   79 NVPRHASFSDVRRFLGRFG----LQPHKTKLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGRPLSV 141
Cdd:smart00360   6 NLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSkGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 102-164 7.02e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 42.49  E-value: 7.02e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1061899871 102 KTKLFGqppcaFVTFRSAAERDKALRVLHGALWKGRPLSVRLARPKADPMARRRRQEGESEPP 164
Cdd:TIGR01628 324 VSRGFG-----FVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPR 381
 
Name Accession Description Interval E-value
TrmA COG2265
tRNA/tmRNA/rRNA uracil-C5-methylase, TrmA/RlmC/RlmD family [Translation, ribosomal structure ...
 178-605 6.64e-64

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: 215.43  E-value: 6.64e-64
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 178 VPYAEQLERKQLECEQVLQKLAKEIGstnrallpwlleqrhkhnkacCPLEGVRPSPQQTEYRNKCEFlvgvGVDGEDNT 257
Cdd:COG2265    81 LSYEAQLELKQRVVREALERIGGLPE---------------------VEVEPIIGSPEPWGYRNRARL----SVRRTDGR 135

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 258 VgcRLGKYKGGTCAVAaPFDTVHI-PEATKQVVKAFQEFIRSTpysaydpETYTGHWKQLTVRtsrrhqamaiayfhpqk 336
Cdd:COG2265   136 L--RLGFYARGSHELV-DIDECPLlDPALNALLPALRELLAEL-------GARRGELRHLVVR----------------- 188

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 337 lspeelaelktslaqhftagpgrasgvtclyfveegqrktpsqeglplehvAGDRCIHEDLLGLTFRISPHAFFQVNTPA 416
Cdd:COG2265   189 ---------------------------------------------------AGRDYLTERLGGLTFRISPGSFFQVNPEQ 217

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 417 AEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNE 496
Cdd:COG2265   218 AEALYAAALEWLDLTGGERVLDLYCGVGTFALPLAR------------------RAKKVIGVEIVPEAVEDARENARLNG 279

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 497 LSNVEFHCGRAEDLVPTLVSRLASQhlVAILDPPRAGLHSKVILAIRRAKnLRRLLYVSCNP----RaamgnfvDLCRAP 572
Cdd:COG2265   280 LKNVEFVAGDLEEVLPELLWGGRPD--VVVLDPPRAGAGPEVLEALAALG-PRRIVYVSCNPatlaR-------DLALLV 349

                         410       420       430
                  ....*....|....*....|....*....|...
gi 1061899871 573 SNRvkgipFRPVKAVAVDLFPQTPHCEMLILFE 605
Cdd:COG2265   350 EGG-----YRLEKVQPVDMFPHTHHVESVALLE 377
RRM_TRMT2A cd12439
RNA recognition motif (RRM) found in tRNA (uracil-5-)-methyltransferase homolog A (TRMT2A) and ...
 68-146 4.69e-40

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: 140.84  E-value: 4.69e-40
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 1061899871  68 FTSEIFKLELQNVPRHASFSDVRRFLGRFGLQPHKTKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGRPLSVRLARP 146
Cdd:cd12439     1 FTSEIFKIEIKNLPKYIGFGQLKKFLQKLGLKPHKIKLIGRQTFAFVTFRNEEDRDKALKVLNGHKWKGKVLSAKLAKP 79
rumA TIGR00479
23S rRNA (uracil-5-)-methyltransferase RumA; This protein family was first proposed to be RNA ...
 178-599 5.51e-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: 149.20  E-value: 5.51e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 178 VPYAEQLERKQLECEQVLQklakeigstnrallpwlleqRHKHNKaccpLEGVRPSPQQTE----YRNKCEFLVGvgvdg 253
Cdd:TIGR00479  72 LSYELQLRSKQQQVIALLE--------------------RIGKFV----SEPIEDVPTIGDdpwgYRNKARLSLG----- 122

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 254 EDNTVGCRLGKYKGGT--------CAVAAPfdtvhipeATKQVVKAFQEFIRSTPYSAYDPETYTGHWKQLTVRTSRRHQ 325
Cdd:TIGR00479 123 RSPSGQLQAGFYQKGShdivdvkqCPVQAP--------ALNALLPKVRAILENFGASRYLEHKELGQARHGVLRIGRHTG 194

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 326 AMAIAyFHPQKLSPEELAELKTSLAQHFTAGPGRASGVTclyfveegQRKTPSQEGLPLEHVAGDRCIHEDLLGLTFRIS 405
Cdd:TIGR00479 195 ELSSV-DRTALERFPHKEELDLYLQPDSPDVKSICQNIN--------PEKTNVIFGEETEVIAGEMPIYDKSGDLSFTFS 265

                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 406 PHAFFQVNTPAAEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARGpmysppwvgrhhaflfqkVKRVIGVELCPEAV 485
Cdd:TIGR00479 266 ARDFIQVNSGQNEKLVDRALEWLELQGEERVLDAYCGMGTFTLPLAKQ------------------AKSVVGVEGVPESV 327

                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 486 EDARVNAQDNELSNVEFHCGRAEDLVPTLVSRLASQHLVaILDPPRAGLHSKVILAIRRAKNlRRLLYVSCNPRAAMGNF 565
Cdd:TIGR00479 328 EKAQQNAELNGIANVTFYHGTLETVLPKQPWAGNGFDKV-LLDPPRKGCAAGVLRTIIKLKP-ERIVYVSCNPATLARDL 405

                         410       420       430
                  ....*....|....*....|....*....|....
gi 1061899871 566 VDLCRApsnrvkgiPFRPVKAVAVDLFPQTPHCE 599
Cdd:TIGR00479 406 EALCKA--------GYTIARVQPVDMFPHTGHVE 431
rumB PRK03522
23S rRNA (uracil(747)-C(5))-methyltransferase RlmC;
385-606 7.40e-24

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


Pssm-ID: 235128 [Multi-domain]  Cd Length: 315  Bit Score: 102.64  E-value: 7.40e-24
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 385 EHVA---GDRCIH--------EDLLGLTFRISPHAFFQVNTPAAEVLYTVIQDW-AQLDAGSMVlDVCCGTGTIGLALAR 452
Cdd:PRK03522  115 VHMAileGEEEIFlteqqalpERFNGVPLFIRPQSFFQTNPAVAAQLYATARDWvRELPPRSMW-DLFCGVGGFGLHCAT 193

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 453 GPMysppwvgrhhaflfqkvkRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRA------EDLVPTLVsrlasqhlvaI 526
Cdd:PRK03522  194 PGM------------------QLTGIEISAEAIACAKQSAAELGLTNVQFQALDStqfataQGEVPDLV----------L 245

                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 527 LDPPRAGLhSKVILAIRRAKNLRRLLYVSCNPrAAMGNfvDLCRAPSnrvkgipFRPVKAVAVDLFPQTPHCEMLILFER 606
Cdd:PRK03522  246 VNPPRRGI-GKELCDYLSQMAPRFILYSSCNA-QTMAK--DLAHLPG-------YRIERVQLFDMFPHTAHYEVLTLLVR 314
rumA PRK13168
23S rRNA (uracil(1939)-C(5))-methyltransferase RlmD;
399-606 1.18e-21

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


Pssm-ID: 237291 [Multi-domain]  Cd Length: 443  Bit Score: 98.30  E-value: 1.18e-21
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 399 GLTFRISPHAFFQVNTPAAEVLytVIQ--DWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVI 476
Cdd:PRK13168  264 GLRLAFSPRDFIQVNAQVNQKM--VARalEWLDPQPGDRVLDLFCGLGNFTLPLAR------------------QAAEVV 323

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 477 GVELCPEAVEDARVNAQDNELSNVEFHCgraEDLVPTLVSRL-ASQHLVAIL-DPPRAGlhskvilAIRRAKNL-----R 549
Cdd:PRK13168  324 GVEGVEAMVERARENARRNGLDNVTFYH---ANLEEDFTDQPwALGGFDKVLlDPPRAG-------AAEVMQALaklgpK 393

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|....*..
gi 1061899871 550 RLLYVSCNPraamgnfVDLCRAPSNRVKGiPFRPVKAVAVDLFPQTPHCEMLILFER 606
Cdd:PRK13168  394 RIVYVSCNP-------ATLARDAGVLVEA-GYRLKRAGMLDMFPHTGHVESMALFER 442
HemK COG2890
Methylase of polypeptide chain release factors [Translation, ribosomal structure and ...
 379-505 1.51e-11

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


Pssm-ID: 442135 [Multi-domain]  Cd Length: 282  Bit Score: 65.56  E-value: 1.51e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 379 QEGLPLEHVAGdrciHEDLLGLTFRISPHAFfqV---NTpaaEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpm 455
Cdd:COG2890    65 AAGEPLAYILG----EAEFYGLEFKVDPGVL--IprpET---EELVELALALLPAGAPPRVLDLGTGSGAIALALAK--- 132

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1061899871 456 YSPPWvgrhhaflfqkvkRVIGVELCPEAVEDARVNAQDNELSN-VEFHCG 505
Cdd:COG2890   133 ERPDA-------------RVTAVDISPDALAVARRNAERLGLEDrVRFLQG 170
AdoMet_MTases cd02440
S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; ...
 436-556 3.15e-11

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: 60.52  E-value: 3.15e-11
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 436 VLDVCCGTGTIGLALARGPmysppwvgrhhaflfqkVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRAEDLVPTLV 515
Cdd:cd02440     2 VLDLGCGTGALALALASGP-----------------GARVTGVDISPVALELARKAAAALLADNVEVLKGDAEELPPEAD 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....
gi 1061899871 516 SRLAsqhlVAILDPP---RAGLHSKVILAIRRAKNLRRLLYVSC 556
Cdd:cd02440    65 ESFD----VIISDPPlhhLVEDLARFLEEARRLLKPGGVLVLTL 104
Methyltransf_25 pfam13649
Methyltransferase domain; This family appears to be a methyltransferase domain.
 436-510 5.90e-11

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


Pssm-ID: 463945 [Multi-domain]  Cd Length: 96  Bit Score: 59.11  E-value: 5.90e-11
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 1061899871 436 VLDVCCGTGTIGLALARgpmysppwvgRHHAflfqkvkRVIGVELCPEAVEDARVNAQDNELsNVEFHCGRAEDL 510
Cdd:pfam13649   1 VLDLGCGTGRLTLALAR----------RGGA-------RVTGVDLSPEMLERARERAAEAGL-NVEFVQGDAEDL 57
PRK09328 PRK09328
N5-glutamine S-adenosyl-L-methionine-dependent methyltransferase; Provisional
 380-505 1.12e-10

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


Pssm-ID: 236467 [Multi-domain]  Cd Length: 275  Bit Score: 62.87  E-value: 1.12e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 380 EGLPLEHVAGdrciHEDLLGLTFRISPHAFfqVNTPAAEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpmYSPP 459
Cdd:PRK09328   62 AGEPLQYILG----EAEFWGLDFKVSPGVL--IPRPETEELVEWALEALLLKEPLRVLDLGTGSGAIALALAK---ERPD 132

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*.
gi 1061899871 460 WvgrhhaflfqkvkRVIGVELCPEAVEDARVNAQDNELSNVEFHCG 505
Cdd:PRK09328  133 A-------------EVTAVDISPEALAVARRNAKHGLGARVEFLQG 165
tRNA_U5-meth_tr pfam05958
tRNA (Uracil-5-)-methyltransferase; This family consists of (Uracil-5-)-methyltransferases EC: ...
 408-607 2.30e-10

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: 62.84  E-value: 2.30e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 408 AFFQVNTPAAEVLYTVIQDWAQLDAGSMvLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVED 487
Cdd:pfam05958 178 SFTQPNAAVNIKMLEWACDVTQGSKGDL-LELYCGNGNFSLALAR------------------NFRKVLATEIAKPSVAA 238

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 488 ARVNAQDNELSNVEFHCGRAEDLVPTLVSRLASQHLVAI-----------LDPPRAGLHSKVIlaiRRAKNLRRLLYVSC 556
Cdd:pfam05958 239 AQYNIAANNIDNVQIIRMSAEEFTQAMNGVREFNRLKGIdlksyncstifVDPPRAGLDPETL---KLVQAYPRILYISC 315

                         170       180       190       200       210
                  ....*....|....*....|....*....|....*....|....*....|.
gi 1061899871 557 NPRAAMGNFVDLCRapSNRVKgipfrpvKAVAVDLFPQTPHCEMLILFERV 607
Cdd:pfam05958 316 NPETLCANLEQLSK--THRVE-------RFALFDQFPYTHHMECGVLLEKK 357
SmtA COG0500
SAM-dependent methyltransferase [Secondary metabolites biosynthesis, transport and catabolism, ...
 415-512 5.81e-10

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


Pssm-ID: 440266 [Multi-domain]  Cd Length: 199  Bit Score: 59.16  E-value: 5.81e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 415 PAAEVLYTVIQDwaqLDAGSMVLDVCCGTGTIGLALARgpmysppwvgRHHAflfqkvkRVIGVELCPEAVEDARVNAQD 494
Cdd:COG0500    12 PGLAALLALLER---LPKGGRVLDLGCGTGRNLLALAA----------RFGG-------RVIGIDLSPEAIALARARAAK 71

                          90
                  ....*....|....*...
gi 1061899871 495 NELSNVEFHCGRAEDLVP 512
Cdd:COG0500    72 AGLGNVEFLVADLAELDP 89
TrmN6 COG4123
tRNA1(Val) A37 N6-methylase TrmN6 [Translation, ribosomal structure and biogenesis]; tRNA1(Val) ...
 426-514 7.00e-10

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: 59.77  E-value: 7.00e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 426 DWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgRHHAflfqkvKRVIGVELCPEAVEDARVNAQDNELSN-VEFHC 504
Cdd:COG4123    31 AFAPVKKGGRVLDLGTGTGVIALMLAQ----------RSPG------ARITGVEIQPEAAELARRNVALNGLEDrITVIH 94

                          90
                  ....*....|
gi 1061899871 505 GRAEDLVPTL 514
Cdd:COG4123    95 GDLKEFAAEL 104
Methyltransf_31 pfam13847
Methyltransferase domain; This family appears to have methyltransferase activity.
 430-557 1.88e-09

Methyltransferase domain; This family appears to have methyltransferase activity.


Pssm-ID: 463998 [Multi-domain]  Cd Length: 150  Bit Score: 56.66  E-value: 1.88e-09
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 430 LDAGSMVLDVCCGTGTIGLALAR--GPMysppwvgrhhaflfqkvKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRA 507
Cdd:pfam13847   1 IDKGMRVLDLGCGTGHLSFELAEelGPN-----------------AEVVGIDISEEAIEKARENAQKLGFDNVEFEQGDI 63

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|..
gi 1061899871 508 EDLvPTLVSR------LASQHLVAILDPPRA------GLHSKVILAIRRAKNLRRLLYVSCN 557
Cdd:pfam13847  64 EEL-PELLEDdkfdvvISNCVLNHIPDPDKVlqeilrVLKPGGRLIISDPDSLAELPAHVKE 124
UbiE COG2226
Ubiquinone/menaquinone biosynthesis C-methylase UbiE/MenG [Coenzyme transport and metabolism]; ...
 426-510 1.05e-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: 54.23  E-value: 1.05e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 426 DWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNELsNVEFHCG 505
Cdd:COG2226    16 AALGLRPGARVLDLGCGTGRLALALAE------------------RGARVTGVDISPEMLELARERAAEAGL-NVEFVVG 76


                  ....*
gi 1061899871 506 RAEDL 510
Cdd:COG2226    77 DAEDL 81
PRK05031 PRK05031
tRNA (uracil-5-)-methyltransferase; Validated
 441-606 1.73e-08

tRNA (uracil-5-)-methyltransferase; Validated


Pssm-ID: 235332  Cd Length: 362  Bit Score: 56.76  E-value: 1.73e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 441 CGTGTIGLALArgpmysppwvgrhhaflfQKVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRAEDLVPTL-----V 515
Cdd:PRK05031  215 CGNGNFTLALA------------------RNFRRVLATEISKPSVAAAQYNIAANGIDNVQIIRMSAEEFTQAMngvreF 276

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 516 SRLASQHLVA-----IL-DPPRAGLHSKVIlaiRRAKNLRRLLYVSCNPRAAMGNFVDLCRapSNRVKgipfrpvKAVAV 589
Cdd:PRK05031  277 NRLKGIDLKSynfstIFvDPPRAGLDDETL---KLVQAYERILYISCNPETLCENLETLSQ--THKVE-------RFALF 344

                         170
                  ....*....|....*..
gi 1061899871 590 DLFPQTPHCEMLILFER 606
Cdd:PRK05031  345 DQFPYTHHMECGVLLEK 361
RsmC COG2813
16S rRNA G1207 methylase RsmC [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 427-551 2.74e-08

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: 54.04  E-value: 2.74e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 427 WAQLDAGSM-------------VLDVCCGTGTIGLALARgpmysppwvgrhhaflFQKVKRVIGVELCPEAVEDARVNAQ 493
Cdd:COG2813    31 RDRLDIGTRlllehlpeplggrVLDLGCGYGVIGLALAK----------------RNPEARVTLVDVNARAVELARANAA 94

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1061899871 494 DNELSNVEFHcgraedlVPTLVSRLASQHLVAIL-DPP-RAGL--HSKVILA-IRRAKnlRRL 551
Cdd:COG2813    95 ANGLENVEVL-------WSDGLSGVPDGSFDLILsNPPfHAGRavDKEVAHAlIADAA--RHL 148
RRM COG0724
RNA recognition motif (RRM) domain [Translation, ribosomal structure and biogenesis];
112-149 1.24e-07

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


Pssm-ID: 440488 [Multi-domain]  Cd Length: 85  Bit Score: 49.33  E-value: 1.24e-07
                          10        20        30
                  ....*....|....*....|....*....|....*...
gi 1061899871 112 AFVTFRSAAERDKALRVLHGALWKGRPLSVRLARPKAD 149
Cdd:COG0724    46 GFVEMPDDEEAQAAIEALNGAELMGRTLKVNEARPREE 83
RRM1_RBM40_like cd12238
RNA recognition motif 1 (RRM1) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 79-141 1.37e-07

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: 49.17  E-value: 1.37e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1061899871  79 NVPRHASFSDVRRFLGRFGLqpHKTKLFGQPP----CAFVTFRSAAERDKALRVLHGALWKGRPLSV 141
Cdd:cd12238     6 HLPPELSEDDKEDLLKHFGA--TSVRVMKRRGklkhTAFATFDNEQAASKALSRLHQLKILGKRLVV 70
RRM_SF cd00590
RNA recognition motif (RRM) superfamily; RRM, also known as RBD (RNA binding domain) or RNP ...
 79-142 1.63e-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: 48.82  E-value: 1.63e-07
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1061899871  79 NVPRHASFSDVRRFLGRFG----LQPHKTKLFGQPPCAFVTFRSAAERDKALRVLHGALWKGRPLSVR 142
Cdd:cd00590     5 NLPPDTTEEDLRELFSKFGevvsVRIVRDRDGKSKGFAFVEFESPEDAEKALEALNGTELGGRPLKVS 72
Tam COG4106
Trans-aconitate methyltransferase [Energy production and conversion];
436-523 2.35e-07

Trans-aconitate methyltransferase [Energy production and conversion];


Pssm-ID: 443282 [Multi-domain]  Cd Length: 100  Bit Score: 49.05  E-value: 2.35e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 436 VLDVCCGTGTIGLALARgpmysppwvgRHHAFlfqkvkRVIGVELCPEAVEDARvnaqdNELSNVEFHCGRAEDLVPT-- 513
Cdd:COG4106     5 VLDLGCGTGRLTALLAE----------RFPGA------RVTGVDLSPEMLARAR-----ARLPNVRFVVADLRDLDPPep 63

                          90
                  ....*....|...
gi 1061899871 514 ---LVSRLASQHL 523
Cdd:COG4106    64 fdlVVSNAALHWL 76
UbiG COG2227
2-polyprenyl-3-methyl-5-hydroxy-6-metoxy-1,4-benzoquinol methylase [Coenzyme transport and ...
 420-510 2.97e-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: 49.63  E-value: 2.97e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 420 LYTVIQDWaqLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVEDARVNAQDnelSN 499
Cdd:COG2227    14 LAALLARL--LPAGGRVLDVGCGTGRLALALAR------------------RGADVTGVDISPEALEIARERAAE---LN 70

                          90
                  ....*....|.
gi 1061899871 500 VEFHCGRAEDL 510
Cdd:COG2227    71 VDFVQGDLEDL 81
PCMT pfam01135
Protein-L-isoaspartate(D-aspartate) O-methyltransferase (PCMT);
426-505 5.08e-07

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


Pssm-ID: 395902 [Multi-domain]  Cd Length: 205  Bit Score: 50.83  E-value: 5.08e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 426 DWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhafLFQKVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCG 505
Cdd:pfam01135  67 ELLELKPGMRVLEIGSGSGYLTACFAR---------------MVGEVGRVVSIEHIPELVEIARRNLEKLGLENVIVVVG 131
RRM smart00360
RNA recognition motif;
79-141 5.28e-06

RNA recognition motif;


Pssm-ID: 214636 [Multi-domain]  Cd Length: 73  Bit Score: 44.51  E-value: 5.28e-06
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1061899871   79 NVPRHASFSDVRRFLGRFG----LQPHKTKLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGRPLSV 141
Cdd:smart00360   6 NLPPDTTEEELRELFSKFGkvesVRLVRDKETGKSkGFAFVEFESEEDAEKALEALNGKELDGRPLKV 73
Trm11 COG1041
tRNA G10 N-methylase Trm11 [Translation, ribosomal structure and biogenesis]; tRNA G10 ...
 428-530 7.73e-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: 46.48  E-value: 7.73e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 428 AQLDAGSMVLDVCCGTGTIglALARGpmysppWVGRhhaflfqkvkRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRA 507
Cdd:COG1041    22 AGAKEGDTVLDPFCGTGTI--LIEAG------LLGR----------RVIGSDIDPKMVEGARENLEHYGYEDADVIRGDA 83

                          90       100
                  ....*....|....*....|....
gi 1061899871 508 EDLvptlvsRLASQHL-VAILDPP 530
Cdd:COG1041    84 RDL------PLADESVdAIVTDPP 101
RRM_RBM18 cd12355
RNA recognition motif (RRM) found in eukaryotic RNA-binding protein 18 and similar proteins; ...
 101-145 1.86e-05

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: 43.06  E-value: 1.86e-05
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*..
gi 1061899871 101 HKT-KLFGQP-PCAFVTFRSAAERDKALRVLHGALWKGRPLSVRLAR 145
Cdd:cd12355    34 HKTgPLKGQPrGYCFVTFETKEEAEKAIECLNGKLALGKKLVVRWAH 80
Cfa COG2230
Cyclopropane fatty-acyl-phospholipid synthase and related methyltransferases [Lipid transport ...
 415-513 2.11e-05

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


Pssm-ID: 441831 [Multi-domain]  Cd Length: 158  Bit Score: 44.92  E-value: 2.11e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 415 PAAEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgRHHAflfqkvkRVIGVELCPEAVEDARVNAQD 494
Cdd:COG2230    34 EAQEAKLDLILRKLGLKPGMRVLDIGCGWGGLALYLAR----------RYGV-------RVTGVTLSPEQLEYARERAAE 96

                          90       100
                  ....*....|....*....|
gi 1061899871 495 NELSN-VEFHCGRAEDLVPT 513
Cdd:COG2230    97 AGLADrVEVRLADYRDLPAD 116
COG2263 COG2263
Predicted RNA methylase [General function prediction only];
411-510 2.19e-05

Predicted RNA methylase [General function prediction only];


Pssm-ID: 441864 [Multi-domain]  Cd Length: 199  Bit Score: 45.67  E-value: 2.19e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 411 QVNTP---AAEVLYTVIqdwAQLD-AGSMVLDVCCGTGTIGLALA-RGPmysppwvgrhhaflfqkvKRVIGVELCPEAV 485
Cdd:COG2263    23 QYPTPaelAAELLHLAY---LRGDiEGKTVLDLGCGTGMLAIGAAlLGA------------------KKVVGVDIDPEAL 81

                          90       100
                  ....*....|....*....|....*
gi 1061899871 486 EDARVNAqDNELSNVEFHCGRAEDL 510
Cdd:COG2263    82 EIARENA-ERLGVRVDFIRADVTRI 105
hemK_fam TIGR00536
HemK family putative methylases; The gene hemK from E. coli was found to contribute to heme ...
 436-530 3.48e-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: 46.19  E-value: 3.48e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 436 VLDVCCGTGTIGLALArgpMYSPPwvgrhhaflfqkvKRVIGVELCPEAVEDARVNAQDNELS-NVEFHCGRaedlvptL 514
Cdd:TIGR00536 118 ILDLGTGSGCIALALA---YEFPN-------------AEVIAVDISPDALAVAEENAEKNQLEhRVEFIQSN-------L 174

                          90
                  ....*....|....*..
gi 1061899871 515 VSRLASQHLVAIL-DPP 530
Cdd:TIGR00536 175 FEPLAGQKIDIIVsNPP 191
MenG_MenH_UbiE TIGR01934
ubiquinone/menaquinone biosynthesis methyltransferases; This model represents a family of ...
 426-510 4.53e-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: 45.33  E-value: 4.53e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 426 DWAQLDAGSMVLDVCCGTGTIGLALARgpmySPPwvgrhhaflfqKVKRVIGVELCPEAVEDARvnAQDNELSNVEFHCG 505
Cdd:TIGR01934  33 KLIGVFKGQKVLDVACGTGDLAIELAK----SAP-----------DRGKVTGVDFSSEMLEVAK--KKSELPLNIEFIQA 95


                  ....*
gi 1061899871 506 RAEDL 510
Cdd:TIGR01934  96 DAEAL 100
RRM2_RBM40_like cd12239
RNA recognition motif 2 (RRM2) found in RNA-binding protein 40 (RBM40) and similar proteins; ...
 74-144 9.83e-05

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: 41.06  E-value: 9.83e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871  74 KLELQNVPRHASFSDVRRFLGRFgLQPHKT-------------KLFGQppcAFVTFRSAAERDKALRVLHGALWKGRPLS 140
Cdd:cd12239     3 RLYVKNLSKRVSEKDLKYIFGRF-VDSSSEeknmfdirlmtegRMKGQ---AFITFPSEELAEKALNLTNGYVLHGKPMV 78


                  ....
gi 1061899871 141 VRLA 144
Cdd:cd12239    79 VQFA 82
RsmD COG0742
16S rRNA G966 N2-methylase RsmD [Translation, ribosomal structure and biogenesis]; 16S rRNA ...
 432-554 1.43e-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: 43.15  E-value: 1.43e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 432 AGSMVLDVCCGTGTIGL-ALARGpmysppwvgrhhaflfqkVKRVIGVELCPEAVEDARVNAQD-NELSNVEFHCGRAED 509
Cdd:COG0742    41 EGARVLDLFAGSGALGLeALSRG------------------AASVVFVEKDRKAAAVIRKNLEKlGLEDRARVIRGDALR 102

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*...
gi 1061899871 510 LVPTLVSRlaSQHLVaILDPP-RAGLHSKVILAIRRAKNLRR--LLYV 554
Cdd:COG0742   103 FLKRLAGE--PFDLV-FLDPPyAKGLLEKALELLAENGLLAPggLIVV 147
Methyltransf_11 pfam08241
Methyltransferase domain; Members of this family are SAM dependent methyltransferases.
 437-510 2.10e-04

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


Pssm-ID: 462406 [Multi-domain]  Cd Length: 94  Bit Score: 40.73  E-value: 2.10e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1061899871 437 LDVCCGTgtiglalargpmysppwvGRHHAFLFQKVKRVIGVELCPEAVEDARVNAQDNelsNVEFHCGRAEDL 510
Cdd:pfam08241   1 LDVGCGT------------------GLLTELLARLGARVTGVDISPEMLELAREKAPRE---GLTFVVGDAEDL 53
RlmK COG1092
23S rRNA G2069 N7-methylase RlmK or C1962 C5-methylase RlmI [Translation, ribosomal structure ...
 379-530 2.21e-04

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


Pssm-ID: 440709 [Multi-domain]  Cd Length: 392  Bit Score: 44.02  E-value: 2.21e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 379 QEGLPLE--HVAGDRC----IHEDllGLTFRISPHA-----FF--QVNTPAAevlytvIQDWAqldAGSMVLDVCCGTGT 445
Cdd:COG1092   161 LEGLPQYegVLYGEAPeeveVEEN--GLKFLVDLTDgqktgLFldQRENRAR------VAELA---KGKRVLNLFSYTGG 229

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 446 IGLALARGpmysppwvGrhhAflfqkvKRVIGVELCPEAVEDARVNAQDNELS-NVEFHCGRAEDLVPTLVSRLASQHLV 524
Cdd:COG1092   230 FSVHAAAG--------G---A------KSVTSVDLSATALEWAKENAALNGLDdRHEFVQADAFDWLRELAREGERFDLI 292


                  ....*.
gi 1061899871 525 aILDPP 530
Cdd:COG1092   293 -ILDPP 297
COG4976 COG4976
Predicted methyltransferase, contains TPR repeat [General function prediction only];
416-510 2.93e-04

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


Pssm-ID: 444001 [Multi-domain]  Cd Length: 181  Bit Score: 42.29  E-value: 2.93e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 416 AAEVLYTVIQDWAQ-------LDAGSMVLDVCCGTGTIGLALArgpmysppwvgrhhaflfQKVKRVIGVELCPEAVEDA 488
Cdd:COG4976    23 VEDLGYEAPALLAEellarlpPGPFGRVLDLGCGTGLLGEALR------------------PRGYRLTGVDLSEEMLAKA 84

                          90       100
                  ....*....|....*....|..
gi 1061899871 489 RVNAQDnelsnVEFHCGRAEDL 510
Cdd:COG4976    85 REKGVY-----DRLLVADLADL 101
ubiE PRK00216
bifunctional demethylmenaquinone methyltransferase/2-methoxy-6-polyprenyl-1,4-benzoquinol ...
 426-510 3.14e-04

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


Pssm-ID: 234689 [Multi-domain]  Cd Length: 239  Bit Score: 42.83  E-value: 3.14e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 426 DWAQLDAGSMVLDVCCGTGTIGLALARGpmysppwVGrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNELS-NVEFHC 504
Cdd:PRK00216   45 KWLGVRPGDKVLDLACGTGDLAIALAKA-------VG--------KTGEVVGLDFSEGMLAVGREKLRDLGLSgNVEFVQ 109


                  ....*.
gi 1061899871 505 GRAEDL 510
Cdd:PRK00216  110 GDAEAL 115
PRK14968 PRK14968
putative methyltransferase; Provisional
 428-502 3.25e-04

putative methyltransferase; Provisional


Pssm-ID: 237872 [Multi-domain]  Cd Length: 188  Bit Score: 42.19  E-value: 3.25e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1061899871 428 AQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNELSN--VEF 502
Cdd:PRK14968   19 AVDKKGDRVLEVGTGSGIVAIVAAK------------------NGKKVVGVDINPYAVECAKCNAKLNNIRNngVEV 77
RRM1_2_CELF1-6_like cd12361
RNA recognition motif 1 (RRM1) and 2 (RRM2) found in CELF/Bruno-like family of RNA binding ...
 74-131 4.15e-04

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: 39.14  E-value: 4.15e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1061899871  74 KLELQNVPRHASFSDVRRFLGRFG----LQPHKTKLFGQPP-CAFVTFRSAAERDKALRVLHG 131
Cdd:cd12361     1 KLFVGMIPKTASEEDVRPLFEQFGnieeVQILRDKQTGQSKgCAFVTFSTREEALRAIEALHN 63
RRM2_NsCP33_like cd21608
RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ...
 112-144 5.59e-04

RNA recognition motif 2 (RRM2) found in Nicotiana sylvestris chloroplastic 33 kDa ribonucleoprotein (NsCP33) and similar proteins; The family includes NsCP33, Arabidopsis thaliana chloroplastic 31 kDa ribonucleoprotein (CP31A) and mitochondrial glycine-rich RNA-binding protein 2 (AtGR-RBP2). NsCP33 may be involved in splicing and/or processing of chloroplast RNA's. AtCP31A, also called RNA-binding protein 1/2/3 (AtRBP33), or RNA-binding protein CP31A, or RNA-binding protein RNP-T, or RNA-binding protein cp31, is required for specific RNA editing events in chloroplasts and stabilizes specific chloroplast mRNAs, as well as for normal chloroplast development under cold stress conditions by stabilizing transcripts of numerous mRNAs under these conditions. CP31A may modulate telomere replication through RNA binding domains. AtGR-RBP2, also called AtRBG2, or glycine-rich protein 2 (AtGRP2), or mitochondrial RNA-binding protein 1a (At-mRBP1a), plays a role in RNA transcription or processing during stress. It binds RNAs and DNAs sequence with a preference to single-stranded nucleic acids. AtGR-RBP2 displays strong affinity to poly(U) sequence. It exerts cold and freezing tolerance, probably by exhibiting an RNA chaperone activity during the cold and freezing adaptation process. Some members in this family contain two RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). The model corresponds to the second RRM motif.


Pssm-ID: 410187 [Multi-domain]  Cd Length: 76  Bit Score: 39.07  E-value: 5.59e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1061899871 112 AFVTFRSAAERDKALRVLHGALWKGRPLSVRLA 144
Cdd:cd21608    44 GFVTFSTAEAAEAAIDALNGKELDGRSIVVNEA 76
RRM_hnRNPH_ESRPs_RBM12_like cd12254
RNA recognition motif (RRM) found in heterogeneous nuclear ribonucleoprotein (hnRNP) H protein ...
 75-142 6.35e-04

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: 38.70  E-value: 6.35e-04
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1061899871  75 LELQNVPRHASFSDVRRFLGRFGLQP--------HKTKLFGQppcAFVTFRSAAERDKALRvLHGALWKGRPLSVR 142
Cdd:cd12254     2 VRLRGLPFSATEEDIRDFFSGLDIPPdgihivydDDGRPTGE---AYVEFASEEDAQRALR-RHKGKMGGRYIEVF 73
RRM3_Prp24 cd12298
RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar ...
 111-143 6.44e-04

RNA recognition motif 3 in fungal pre-messenger RNA splicing protein 24 (Prp24) and similar proteins; This subfamily corresponds to the RRM3 of Prp24, also termed U4/U6 snRNA-associated-splicing factor PRP24 (U4/U6 snRNP), an RNA-binding protein with four well conserved RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains). It facilitates U6 RNA base-pairing with U4 RNA during spliceosome assembly. Prp24 specifically binds free U6 RNA primarily with RRMs 1 and 2 and facilitates pairing of U6 RNA bases with U4 RNA bases. Additionally, it may also be involved in dissociation of the U4/U6 complex during spliceosome activation.


Pssm-ID: 409739 [Multi-domain]  Cd Length: 78  Bit Score: 38.78  E-value: 6.44e-04
                          10        20        30
                  ....*....|....*....|....*....|...
gi 1061899871 111 CAFVTFRSAAERDKALRvLHGALWKGRPLSVRL 143
Cdd:cd12298    47 FAFVTFEDADSAESALQ-LNGTLLDNRKISVSL 78
Cons_hypoth95 pfam03602
Conserved hypothetical protein 95;
427-549 6.88e-04

Conserved hypothetical protein 95;


Pssm-ID: 427391 [Multi-domain]  Cd Length: 179  Bit Score: 41.07  E-value: 6.88e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 427 WAQLDAGSMVLDVCCGTGTIGL-ALARGpmysppwvgrhhaflfqkVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCG 505
Cdd:pfam03602  36 LAPYIEGARVLDLFAGSGALGLeALSRG------------------AKRVTLVEKDKRAVQILKENLQLLGLPGAVLVMD 97

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1061899871 506 RAEDLvPTLVSRLASQHLVaILDPP-RAGLHSKVILAIRRAKNLR 549
Cdd:pfam03602  98 ALLAL-LRLAGKGPVFDIV-FLDPPyAKGLIEEVLDLLAEKGWLK 140
PABP-1234 TIGR01628
polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins ...
 102-164 7.02e-04

polyadenylate binding protein, human types 1, 2, 3, 4 family; These eukaryotic proteins recognize the poly-A of mRNA and consists of four tandem RNA recognition domains at the N-terminus (rrm: pfam00076) followed by a PABP-specific domain (pfam00658) at the C-terminus. The protein is involved in the transport of mRNA's from the nucleus to the cytoplasm. There are four paralogs in Homo sapiens which are expressed in testis, platelets, broadly expressed and of unknown tissue range.


Pssm-ID: 130689 [Multi-domain]  Cd Length: 562  Bit Score: 42.49  E-value: 7.02e-04
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1061899871 102 KTKLFGqppcaFVTFRSAAERDKALRVLHGALWKGRPLSVRLARPKADPMARRRRQEGESEPP 164
Cdd:TIGR01628 324 VSRGFG-----FVCFSNPEEANRAVTEMHGRMLGGKPLYVALAQRKEQRRAHLQDQFMQLQPR 381
MTS pfam05175
Methyltransferase small domain; This domain is found in ribosomal RNA small subunit ...
 427-503 8.11e-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: 40.65  E-value: 8.11e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 427 WAQLDAGS-------------MVLDVCCGTGTIGLALARgpmysppwvgrhhaflFQKVKRVIGVELCPEAVEDARVNAQ 493
Cdd:pfam05175  13 HGRLDIGSrlllehlpkdlsgKVLDLGCGAGVLGAALAK----------------ESPDAELTMVDINARALESARENLA 76

                          90
                  ....*....|
gi 1061899871 494 DNELSNVEFH 503
Cdd:pfam05175  77 ANGLENGEVV 86
RRM1_RBM28_like cd12413
RNA recognition motif 1 (RRM1) found in RNA-binding protein 28 (RBM28) and similar proteins; ...
 107-147 1.26e-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: 37.96  E-value: 1.26e-03
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....
gi 1061899871 107 GQPPC---AFVTFRSAAERDKALRVLHGALWKGRPLSVRLARPK 147
Cdd:cd12413    36 GKDKCrgfGYVTFALAEDAQRALEEVKGKKFGGRKIKVELAKKK 79
COG2521 COG2521
Predicted archaeal methyltransferase [General function prediction only];
433-534 1.42e-03

Predicted archaeal methyltransferase [General function prediction only];


Pssm-ID: 442011 [Multi-domain]  Cd Length: 285  Bit Score: 41.05  E-value: 1.42e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 433 GSMVLDVCCGTG--TIGlALARGpmysppwvgrhhaflfqkVKRVIGVELCPEAVEDARVNAQDNELSN--VEFHCGRAE 508
Cdd:COG2521   133 GDRVLDTCTGLGytAIE-ALKRG------------------AREVITVEKDPNVLELAELNPWSRELANerIKIILGDAS 193

                          90       100
                  ....*....|....*....|....*..
gi 1061899871 509 DLVPtlvsRLASQHLVAIL-DPPRAGL 534
Cdd:COG2521   194 EVIK----TFPDESFDAIIhDPPRFSL 216
PRK08317 PRK08317
hypothetical protein; Provisional
 414-532 1.48e-03

hypothetical protein; Provisional


Pssm-ID: 181382 [Multi-domain]  Cd Length: 241  Bit Score: 40.69  E-value: 1.48e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 414 TPAAEVLYTVIQDWAQLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhafLFQKVKRVIGVELCPEAVEDARvNAQ 493
Cdd:PRK08317    1 LPDFRRYRARTFELLAVQPGDRVLDVGCGPGNDARELAR---------------RVGPEGRVVGIDRSEAMLALAK-ERA 64

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|....*
gi 1061899871 494 DNELSNVEFHCGRAEDL------VPTLVSRLASQHlvaILDPPRA 532
Cdd:PRK08317   65 AGLGPNVEFVRGDADGLpfpdgsFDAVRSDRVLQH---LEDPARA 106
arsM PRK11873
arsenite methyltransferase;
428-510 1.61e-03

arsenite methyltransferase;


Pssm-ID: 237007 [Multi-domain]  Cd Length: 272  Bit Score: 40.70  E-value: 1.61e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 428 AQLDAGSMVLDVCCGTGtIGLALARgpmyspPWVGrhhaflfqKVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRA 507
Cdd:PRK11873   73 AELKPGETVLDLGSGGG-FDCFLAA------RRVG--------PTGKVIGVDMTPEMLAKARANARKAGYTNVEFRLGEI 137


                  ...
gi 1061899871 508 EDL 510
Cdd:PRK11873  138 EAL 140
Ubie_methyltran pfam01209
ubiE/COQ5 methyltransferase family;
433-510 1.74e-03

ubiE/COQ5 methyltransferase family;


Pssm-ID: 395966 [Multi-domain]  Cd Length: 228  Bit Score: 40.50  E-value: 1.74e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1061899871 433 GSMVLDVCCGTGTIGLALARgpmysppwvgrhhafLFQKVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRAEDL 510
Cdd:pfam01209  43 GNKFLDVAGGTGDWTFGLSD---------------SAGSSGKVVGLDINENMLKEGEKKAKEEGKYNIEFLQGNAEEL 105
RRM_FOX1_like cd12407
RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar ...
 74-144 2.08e-03

RNA recognition motif (RRM) found in vertebrate RNA binding protein fox-1 homologs and similar proteins; This subfamily corresponds to the RRM of several tissue-specific alternative splicing isoforms of vertebrate RNA binding protein Fox-1 homologs, which show high sequence similarity to the Caenorhabditis elegans feminizing locus on X (Fox-1) gene encoding Fox-1 protein. RNA binding protein Fox-1 homolog 1 (RBFOX1), also termed ataxin-2-binding protein 1 (A2BP1), or Fox-1 homolog A, or hexaribonucleotide-binding protein 1 (HRNBP1), is predominantly expressed in neurons, skeletal muscle and heart. It regulates alternative splicing of tissue-specific exons by binding to UGCAUG elements. Moreover, RBFOX1 binds to the C-terminus of ataxin-2 and forms an ataxin-2/A2BP1 complex involved in RNA processing. RNA binding protein fox-1 homolog 2 (RBFOX2), also termed Fox-1 homolog B, or hexaribonucleotide-binding protein 2 (HRNBP2), or RNA-binding motif protein 9 (RBM9), or repressor of tamoxifen transcriptional activity, is expressed in ovary, whole embryo, and human embryonic cell lines in addition to neurons and muscle. RBFOX2 activates splicing of neuron-specific exons through binding to downstream UGCAUG elements. RBFOX2 also functions as a repressor of tamoxifen activation of the estrogen receptor. RNA binding protein Fox-1 homolog 3 (RBFOX3 or NeuN or HRNBP3), also termed Fox-1 homolog C, is a nuclear RNA-binding protein that regulates alternative splicing of the RBFOX2 pre-mRNA, producing a message encoding a dominant negative form of the RBFOX2 protein. Its message is detected exclusively in post-mitotic regions of embryonic brain. Like RBFOX1, both RBFOX2 and RBFOX3 bind to the hexanucleotide UGCAUG elements and modulate brain and muscle-specific splicing of exon EIIIB of fibronectin, exon N1 of c-src, and calcitonin/CGRP. Members in this family also harbor one RNA recognition motifs (RRMs), also termed RBDs (RNA binding domains) or RNPs (ribonucleoprotein domains).


Pssm-ID: 409841 [Multi-domain]  Cd Length: 76  Bit Score: 37.38  E-value: 2.08e-03
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1061899871  74 KLELQNVPRHASFSDVRRFLGRFGLQPHKTKLF---GQPPCAFVTFRSAAERDKALRVLHGALWKGRPLSVRLA 144
Cdd:cd12407     2 RLHVSNIPFRFRDPDLRQMFGQFGTILDVEIIFnerGSKGFGFVTFANSADADRAREKLNGTVVEGRKIEVNNA 75
RRM_NOL8 cd12226
RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This ...
 84-145 3.20e-03

RNA recognition motif (RRM) found in nucleolar protein 8 (NOL8) and similar proteins; This model corresponds to the RRM of NOL8 (also termed Nop132) encoded by a novel NOL8 gene that is up-regulated in the majority of diffuse-type, but not intestinal-type, gastric cancers. Thus, NOL8 may be a good molecular target for treatment of diffuse-type gastric cancer. Also, NOL8 is a phosphorylated protein that contains an N-terminal RNA recognition motif (RRM), also known as RBD (RNA binding domain) or RNP (ribonucleoprotein domain), suggesting NOL8 is likely to function as a novel RNA-binding protein. It may be involved in regulation of gene expression at the post-transcriptional level or in ribosome biogenesis in cancer cells.


Pssm-ID: 409673 [Multi-domain]  Cd Length: 77  Bit Score: 36.79  E-value: 3.20e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1061899871  84 ASFSDVRRFLGRFG----LQPHKTKLFGQPPCAFVTFR-SAAERDKALRVLHGALWKGRPLSVRLAR 145
Cdd:cd12226    11 ITEDDLERRFSRFGtvsdVEIIRKKDAPDRGFAYIDLRtSEAALQKCLSTLNGVKWKGSRLKIQLAK 77
CobL COG2242
Precorrin-6B methylase 2 [Coenzyme transport and metabolism]; Precorrin-6B methylase 2 is part ...
 429-509 3.89e-03

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: 40.15  E-value: 3.89e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 429 QLDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflFQKVKRVIGVELCPEAVEDARVNAQDNELSNVEFHCGRAE 508
Cdd:COG2242   244 ALRPGDVLWDIGAGSGSVSIEAAR----------------LAPGGRVYAIERDPERAALIRANARRFGVPNVEVVEGEAP 307


                  .
gi 1061899871 509 D 509
Cdd:COG2242   308 E 308
PRK14967 PRK14967
putative methyltransferase; Provisional
 430-492 4.29e-03

putative methyltransferase; Provisional


Pssm-ID: 184931 [Multi-domain]  Cd Length: 223  Bit Score: 39.27  E-value: 4.29e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 1061899871 430 LDAGSMVLDVCCGTGTIGLALARgpmysppwvgrhhaflfQKVKRVIGVELCPEAVEDARVNA 492
Cdd:PRK14967   34 LGPGRRVLDLCTGSGALAVAAAA-----------------AGAGSVTAVDISRRAVRSARLNA 79
PrmA COG2264
Ribosomal protein L11 methylase PrmA [Translation, ribosomal structure and biogenesis];
428-511 4.57e-03

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


Pssm-ID: 441865 [Multi-domain]  Cd Length: 284  Bit Score: 39.39  E-value: 4.57e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1061899871 428 AQLDAGSMVLDVCCGTGtIgLALA---RGPmysppwvgrhhaflfqkvKRVIGVELCPEAVEDARVNAQDNELSN-VEFH 503
Cdd:COG2264   144 KLLKPGKTVLDVGCGSG-I-LAIAaakLGA------------------KRVLAVDIDPVAVEAARENAELNGVEDrIEVV 203

                          90
                  ....*....|...
gi 1061899871 504 CGRAE-----DLV 511
Cdd:COG2264   204 LGDLLedgpyDLV 216
 
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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