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Conserved domains on  [gi|19920684|ref|NP_608834|]
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elongator complex protein 3 [Drosophila melanogaster]

Protein Classification

elongator complex protein 3( domain architecture ID 1003394)

elongator complex protein 3 is the catalytic histone acetyltransferase subunit of the RNA polymerase II elongator complex, which is a component of the RNA polymerase II holoenzyme and is involved in transcriptional elongation

EC:  2.3.1.-
Gene Ontology:  GO:0046872|GO:0016407|GO:0006357

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
ELP3 super family cl36845
radical SAM enzyme/protein acetyltransferase, ELP3 family; This family includes elongator ...
23-548 0e+00

radical SAM enzyme/protein acetyltransferase, ELP3 family; This family includes elongator complex protein 3 (ELP3) from eukaryotes and related proteins from other lineages. ELP3 is a component of the RNA polymerase II holoenzyme. It has an N-terminal radical SAM domain and C-terminal GNAT acetyltransferase domain. Members of this family are found in eukaryotes, archaea, and a few bacteria (e.g. Atopobium sp). The activity discovered first was an acetyltransferase modification at the N-termini of all four core histones, shown in vitro in eukaryotes. More recently, the radical SAM domain was shown to play a role in zygotic paternal genome demethylation. Family TIGR01212, widespread in prokaryotes, lacks the GNAT acetyltransferase domain but shares extensive sequence similarity with this family (TIGR01211). [Transcription, DNA-dependent RNA polymerase]


The actual alignment was detected with superfamily member TIGR01211:

Pssm-ID: 273503 [Multi-domain]  Cd Length: 522  Bit Score: 752.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    23 EIIQELLKAhEAKKDVNLNRMKSLVASKYGLDSSPRLVDIIAAVPQDAKKILLPKLRAKPIRTASGIAVVAVMCKPHRCP 102
Cdd:TIGR01211   1 EIVDSLLSG-KTRDKEDLEDLKLEVSRKYGLSKVPSNSEILNSAPDEEKKKLEPILRKKPVRTISGVAVVAVMTSPHRCP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   103 HINmtgniCVYCPGGPDSdfEYSTQSYTGYEPTSMRAIRSRYDPFLQTRHRVEQLKQLGHSVDKVEFIVMGGTFMCLPEE 182
Cdd:TIGR01211  80 HGK-----CLYCPGGPDS--ENSPQSYTGYEPAAMRGRQNDYDPYEQVTARLEQLEQIGHPVDKVELIIMGGTFPARDLD 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   183 YRDYFIRNLHDALSGHSSA-----NVAEAVRYSEKSRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVA 257
Cdd:TIGR01211 153 YQEWFIKRCLNAMNGFDQElkgnsTLEEAIRINETSKHRCVGLTIETRPDYCREEHIDRMLKLGATRVELGVQTIYNDIL 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   258 RDTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIEYFENPAFRSDGLKIYPTLVIRGTGLYELWKTG 337
Cdd:TIGR01211 233 ERTKRGHTVRDVVEATRLLRDAGLKVVYHIMPGLPGSSFERDLEMFREIFEDPRFKPDMLKIYPTLVTRGTELYELWKRG 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   338 RYKSYPPSMLVDLVAKILALVPPWTRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGTTCRDVRTREVGIQEIHNKV 417
Cdd:TIGR01211 313 EYKPYTTEEAVELIVEIKRMMPKWVRIQRIQRDIPAPLIVAGVKKSNLRELVYRRMKEHGITCRCIRCREVGHQMVKPVQ 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   418 RPYE-IELIRRDYVANGGWETFLSYEDPEQDILVGLLRLRKCSPDTFRPELKGEcSIVRELHVYGSVVPVNARDPTKFQH 496
Cdd:TIGR01211 393 PEEEnVELIVEEYAASGGTEFFLSYEDPKNDILIGFLRLRFPSEPAHRKEVDAT-ALVRELHVYGSEVPIGERGDDEWQH 471
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|..
gi 19920684   497 QGFGMLLMeEAERIAREEHGSTKLAVISGVGTRNYYRKMGYQLDGPYMSKSI 548
Cdd:TIGR01211 472 RGYGRRLL-EEAERIAAEEGSEKILVISGIGVREYYRKLGYELDGPYMSKRL 522
 
Name Accession Description Interval E-value
ELP3 TIGR01211
radical SAM enzyme/protein acetyltransferase, ELP3 family; This family includes elongator ...
23-548 0e+00

radical SAM enzyme/protein acetyltransferase, ELP3 family; This family includes elongator complex protein 3 (ELP3) from eukaryotes and related proteins from other lineages. ELP3 is a component of the RNA polymerase II holoenzyme. It has an N-terminal radical SAM domain and C-terminal GNAT acetyltransferase domain. Members of this family are found in eukaryotes, archaea, and a few bacteria (e.g. Atopobium sp). The activity discovered first was an acetyltransferase modification at the N-termini of all four core histones, shown in vitro in eukaryotes. More recently, the radical SAM domain was shown to play a role in zygotic paternal genome demethylation. Family TIGR01212, widespread in prokaryotes, lacks the GNAT acetyltransferase domain but shares extensive sequence similarity with this family (TIGR01211). [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273503 [Multi-domain]  Cd Length: 522  Bit Score: 752.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    23 EIIQELLKAhEAKKDVNLNRMKSLVASKYGLDSSPRLVDIIAAVPQDAKKILLPKLRAKPIRTASGIAVVAVMCKPHRCP 102
Cdd:TIGR01211   1 EIVDSLLSG-KTRDKEDLEDLKLEVSRKYGLSKVPSNSEILNSAPDEEKKKLEPILRKKPVRTISGVAVVAVMTSPHRCP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   103 HINmtgniCVYCPGGPDSdfEYSTQSYTGYEPTSMRAIRSRYDPFLQTRHRVEQLKQLGHSVDKVEFIVMGGTFMCLPEE 182
Cdd:TIGR01211  80 HGK-----CLYCPGGPDS--ENSPQSYTGYEPAAMRGRQNDYDPYEQVTARLEQLEQIGHPVDKVELIIMGGTFPARDLD 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   183 YRDYFIRNLHDALSGHSSA-----NVAEAVRYSEKSRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVA 257
Cdd:TIGR01211 153 YQEWFIKRCLNAMNGFDQElkgnsTLEEAIRINETSKHRCVGLTIETRPDYCREEHIDRMLKLGATRVELGVQTIYNDIL 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   258 RDTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIEYFENPAFRSDGLKIYPTLVIRGTGLYELWKTG 337
Cdd:TIGR01211 233 ERTKRGHTVRDVVEATRLLRDAGLKVVYHIMPGLPGSSFERDLEMFREIFEDPRFKPDMLKIYPTLVTRGTELYELWKRG 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   338 RYKSYPPSMLVDLVAKILALVPPWTRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGTTCRDVRTREVGIQEIHNKV 417
Cdd:TIGR01211 313 EYKPYTTEEAVELIVEIKRMMPKWVRIQRIQRDIPAPLIVAGVKKSNLRELVYRRMKEHGITCRCIRCREVGHQMVKPVQ 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   418 RPYE-IELIRRDYVANGGWETFLSYEDPEQDILVGLLRLRKCSPDTFRPELKGEcSIVRELHVYGSVVPVNARDPTKFQH 496
Cdd:TIGR01211 393 PEEEnVELIVEEYAASGGTEFFLSYEDPKNDILIGFLRLRFPSEPAHRKEVDAT-ALVRELHVYGSEVPIGERGDDEWQH 471
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|..
gi 19920684   497 QGFGMLLMeEAERIAREEHGSTKLAVISGVGTRNYYRKMGYQLDGPYMSKSI 548
Cdd:TIGR01211 472 RGYGRRLL-EEAERIAAEEGSEKILVISGIGVREYYRKLGYELDGPYMSKRL 522
ELP3 COG1243
tRNA U34 5-carboxymethylaminomethylation enzyme Elp3 (RNA elongator complex protein 3), ...
81-548 0e+00

tRNA U34 5-carboxymethylaminomethylation enzyme Elp3 (RNA elongator complex protein 3), contains radical SAM and acetyltransferase domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440856 [Multi-domain]  Cd Length: 432  Bit Score: 528.33  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  81 KPIRTASGIAVVAVMCKPHRCPHInmtgniCVYCPGGPDSdfeysTQSYTGYEPTSMRAIRSRYDPFLQTRHRVEQLKQL 160
Cdd:COG1243   2 KPVRTISGVAIIPVFTPPAGCPGK------CVFCPQGKIT-----PQSYTGQEPAALRARQNDYDPYKQVRARLEQLLAI 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 161 GHSVDKVEFIVMGGTFMCLPEEYRDYFIRNLHDALSGHSSANVAEAVRYSEKSRTKCIGITIETRPDYCLKRHISDMLSY 240
Cdd:COG1243  71 GHPVDKVELAFMGGTFTALPRDYQEWFLKRALDAMNGFDSPTLEEAQRRNETAEGRIVGIRLETRPDYIDEEILDRLLEY 150
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 241 GCTRLEIGVQSVYEDVARDTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIEYFENpAFRSDGLKIY 320
Cdd:COG1243 151 GVTKVELGVQSLDDEVLKRSNRGHTVEDVIEATRLLRDAGFKVGYHLMPGLPGSTPEKDLETFRELFED-DFRPDMLKIY 229
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 321 PTLVIRGTGLYELWKTGRYKSYPPSMLVDLVAKIL-ALVPPWTRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGTT 399
Cdd:COG1243 230 PTLVIKGTELYELYKRGEYKPLTLEEAVELLAEIKlKFIPRYVRVIRIGRDIPAKEIVAGPKHPNLRQLVESRLEEEGIK 309
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 400 CRDVRTREVGIQEihnkvRPYEIELIRRDYVANGGWETFLSYEDPEQDILVGLLRLRKcsPDTfrpelkgecSIVRELHV 479
Cdd:COG1243 310 CRCIRCREVGHND-----DPEDIELRREDYEASGGKEHFLSFEDKDIDILIGFLRLRF--PKT---------ALVRELHV 373
                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19920684 480 YGSVvpvnardptKFQHQGFGMLLMEEAERIAREEhGSTKLAVISGVGTRNYYRKMGYQLDGPYMSKSI 548
Cdd:COG1243 374 KGNG---------SWQHRGYGKRLLEEAEEIAREE-GYKKLAVISGIGVREYYRKLGYERDGPYMSKDL 432
Radical_SAM_C pfam16199
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of ...
315-392 3.59e-24

Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.


Pssm-ID: 465061 [Multi-domain]  Cd Length: 83  Bit Score: 96.31  E-value: 3.59e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19920684   315 DGLKIYPTLVIRGTGLYELWKTGRYKSYPPSMLVDLVAKILALVPPWTRVYRVQRDIPMPLVSSGVEHG-NLRELALAR 392
Cdd:pfam16199   2 DGVKIHPLLVLKGTPLAELYERGEYKPLSLEEYVELVADFLELLPPDIVIHRLGGDAPKELLVAPPWHLpKFRVLNLVE 80
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
91-351 7.81e-22

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 94.01  E-value: 7.81e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684     91 VVAVMCKPHRCPHInmtgniCVYCpggpdsdfeystqsytgYEPTSMRAIRSRYdpfLQTRHR-VEQLKQLGHSVDKVEF 169
Cdd:smart00729   1 PLALYIITRGCPRR------CTFC-----------------SFPSLRGKLRSRY---LEALVReIELLAEKGEKEGLVGT 54
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    170 IVM-GGTFMCLPEEYRDYFIRNLHDalsghssanvaeavrysEKSRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIG 248
Cdd:smart00729  55 VFIgGGTPTLLSPEQLEELLEAIRE-----------------ILGLAKDVEITIETRPDTLTEELLEALKEAGVNRVSLG 117
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    249 VQSVYEDVARDTNRGHTVRAVCESFQLGKDAG-YKIVTHMMPDLPNVDFErDIEQFIEYFEnpAFRSDGLKIYPTLVIRG 327
Cdd:smart00729 118 VQSGDDEVLKAINRGHTVEDVLEAVELLREAGpIKVSTDLIVGLPGETEE-DFEETLKLLK--ELGPDRVSIFPLSPRPG 194
                          250       260
                   ....*....|....*....|....
gi 19920684    328 TGLYELWKtgRYKSYPPSMLVDLV 351
Cdd:smart00729 195 TPLAKMYK--RLKPPTKEERAELL 216
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
98-346 1.45e-12

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 66.97  E-value: 1.45e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  98 PHRCPHInmtgniCVYCPGGPDSDFEYSTQSYTGYEptsmrairsrydpflqtRHRVEQLKQLGHSVdkveFIVMGGTfm 177
Cdd:cd01335   4 TRGCNLN------CGFCSNPASKGRGPESPPEIEEI-----------------LDIVLEAKERGVEV----VILTGGE-- 54
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 178 CLPEEYRDYFIRNLHDalsghssanvaeavryseksRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVA 257
Cdd:cd01335  55 PLLYPELAELLRRLKK--------------------ELPGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVA 114
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 258 RDTN-RGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIeyFENPAFRSDGLKIYPTLVIRGTGLYELWKT 336
Cdd:cd01335 115 DKIRgSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELE--LLAEFRSPDRVSLFRLLPEEGTPLELAAPV 192
                       250
                ....*....|
gi 19920684 337 GRYKSYPPSM 346
Cdd:cd01335 193 VPAEKLLRLI 202
PRK08208 PRK08208
coproporphyrinogen III oxidase family protein;
218-399 2.45e-05

coproporphyrinogen III oxidase family protein;


Pssm-ID: 181292 [Multi-domain]  Cd Length: 430  Bit Score: 46.93  E-value: 2.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  218 IGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVARDTNRGHTVRAVCESFQLGKDAGYkivthmmPDLpNVD-- 295
Cdd:PRK08208 128 IPKSVETSPATTTAEKLALLAARGVNRLSIGVQSFHDSELHALHRPQKRADVHQALEWIRAAGF-------PIL-NIDli 199
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  296 ----------FERDIEQFIEYfenpafRSDGLKIYPTLVIRGTGLYElwktgRYKSYPPSMLvdlvakilalvppwtRVY 365
Cdd:PRK08208 200 ygipgqthasWMESLDQALVY------RPEELFLYPLYVRPLTGLGR-----RARAWDDQRL---------------SLY 253
                        170       180       190
                 ....*....|....*....|....*....|....
gi 19920684  366 RVQRDIpmpLVSSGVEHGNLRELALARMKDLGTT 399
Cdd:PRK08208 254 RLARDL---LLEAGYTQTSMRMFRRNDAPDKGAP 284
 
Name Accession Description Interval E-value
ELP3 TIGR01211
radical SAM enzyme/protein acetyltransferase, ELP3 family; This family includes elongator ...
23-548 0e+00

radical SAM enzyme/protein acetyltransferase, ELP3 family; This family includes elongator complex protein 3 (ELP3) from eukaryotes and related proteins from other lineages. ELP3 is a component of the RNA polymerase II holoenzyme. It has an N-terminal radical SAM domain and C-terminal GNAT acetyltransferase domain. Members of this family are found in eukaryotes, archaea, and a few bacteria (e.g. Atopobium sp). The activity discovered first was an acetyltransferase modification at the N-termini of all four core histones, shown in vitro in eukaryotes. More recently, the radical SAM domain was shown to play a role in zygotic paternal genome demethylation. Family TIGR01212, widespread in prokaryotes, lacks the GNAT acetyltransferase domain but shares extensive sequence similarity with this family (TIGR01211). [Transcription, DNA-dependent RNA polymerase]


Pssm-ID: 273503 [Multi-domain]  Cd Length: 522  Bit Score: 752.35  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    23 EIIQELLKAhEAKKDVNLNRMKSLVASKYGLDSSPRLVDIIAAVPQDAKKILLPKLRAKPIRTASGIAVVAVMCKPHRCP 102
Cdd:TIGR01211   1 EIVDSLLSG-KTRDKEDLEDLKLEVSRKYGLSKVPSNSEILNSAPDEEKKKLEPILRKKPVRTISGVAVVAVMTSPHRCP 79
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   103 HINmtgniCVYCPGGPDSdfEYSTQSYTGYEPTSMRAIRSRYDPFLQTRHRVEQLKQLGHSVDKVEFIVMGGTFMCLPEE 182
Cdd:TIGR01211  80 HGK-----CLYCPGGPDS--ENSPQSYTGYEPAAMRGRQNDYDPYEQVTARLEQLEQIGHPVDKVELIIMGGTFPARDLD 152
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   183 YRDYFIRNLHDALSGHSSA-----NVAEAVRYSEKSRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVA 257
Cdd:TIGR01211 153 YQEWFIKRCLNAMNGFDQElkgnsTLEEAIRINETSKHRCVGLTIETRPDYCREEHIDRMLKLGATRVELGVQTIYNDIL 232
                         250       260       270       280       290       300       310       320
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   258 RDTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIEYFENPAFRSDGLKIYPTLVIRGTGLYELWKTG 337
Cdd:TIGR01211 233 ERTKRGHTVRDVVEATRLLRDAGLKVVYHIMPGLPGSSFERDLEMFREIFEDPRFKPDMLKIYPTLVTRGTELYELWKRG 312
                         330       340       350       360       370       380       390       400
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   338 RYKSYPPSMLVDLVAKILALVPPWTRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGTTCRDVRTREVGIQEIHNKV 417
Cdd:TIGR01211 313 EYKPYTTEEAVELIVEIKRMMPKWVRIQRIQRDIPAPLIVAGVKKSNLRELVYRRMKEHGITCRCIRCREVGHQMVKPVQ 392
                         410       420       430       440       450       460       470       480
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   418 RPYE-IELIRRDYVANGGWETFLSYEDPEQDILVGLLRLRKCSPDTFRPELKGEcSIVRELHVYGSVVPVNARDPTKFQH 496
Cdd:TIGR01211 393 PEEEnVELIVEEYAASGGTEFFLSYEDPKNDILIGFLRLRFPSEPAHRKEVDAT-ALVRELHVYGSEVPIGERGDDEWQH 471
                         490       500       510       520       530
                  ....*....|....*....|....*....|....*....|....*....|..
gi 19920684   497 QGFGMLLMeEAERIAREEHGSTKLAVISGVGTRNYYRKMGYQLDGPYMSKSI 548
Cdd:TIGR01211 472 RGYGRRLL-EEAERIAAEEGSEKILVISGIGVREYYRKLGYELDGPYMSKRL 522
ELP3 COG1243
tRNA U34 5-carboxymethylaminomethylation enzyme Elp3 (RNA elongator complex protein 3), ...
81-548 0e+00

tRNA U34 5-carboxymethylaminomethylation enzyme Elp3 (RNA elongator complex protein 3), contains radical SAM and acetyltransferase domains [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440856 [Multi-domain]  Cd Length: 432  Bit Score: 528.33  E-value: 0e+00
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  81 KPIRTASGIAVVAVMCKPHRCPHInmtgniCVYCPGGPDSdfeysTQSYTGYEPTSMRAIRSRYDPFLQTRHRVEQLKQL 160
Cdd:COG1243   2 KPVRTISGVAIIPVFTPPAGCPGK------CVFCPQGKIT-----PQSYTGQEPAALRARQNDYDPYKQVRARLEQLLAI 70
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 161 GHSVDKVEFIVMGGTFMCLPEEYRDYFIRNLHDALSGHSSANVAEAVRYSEKSRTKCIGITIETRPDYCLKRHISDMLSY 240
Cdd:COG1243  71 GHPVDKVELAFMGGTFTALPRDYQEWFLKRALDAMNGFDSPTLEEAQRRNETAEGRIVGIRLETRPDYIDEEILDRLLEY 150
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 241 GCTRLEIGVQSVYEDVARDTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIEYFENpAFRSDGLKIY 320
Cdd:COG1243 151 GVTKVELGVQSLDDEVLKRSNRGHTVEDVIEATRLLRDAGFKVGYHLMPGLPGSTPEKDLETFRELFED-DFRPDMLKIY 229
                       250       260       270       280       290       300       310       320
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 321 PTLVIRGTGLYELWKTGRYKSYPPSMLVDLVAKIL-ALVPPWTRVYRVQRDIPMPLVSSGVEHGNLRELALARMKDLGTT 399
Cdd:COG1243 230 PTLVIKGTELYELYKRGEYKPLTLEEAVELLAEIKlKFIPRYVRVIRIGRDIPAKEIVAGPKHPNLRQLVESRLEEEGIK 309
                       330       340       350       360       370       380       390       400
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 400 CRDVRTREVGIQEihnkvRPYEIELIRRDYVANGGWETFLSYEDPEQDILVGLLRLRKcsPDTfrpelkgecSIVRELHV 479
Cdd:COG1243 310 CRCIRCREVGHND-----DPEDIELRREDYEASGGKEHFLSFEDKDIDILIGFLRLRF--PKT---------ALVRELHV 373
                       410       420       430       440       450       460
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19920684 480 YGSVvpvnardptKFQHQGFGMLLMEEAERIAREEhGSTKLAVISGVGTRNYYRKMGYQLDGPYMSKSI 548
Cdd:COG1243 374 KGNG---------SWQHRGYGKRLLEEAEEIAREE-GYKKLAVISGIGVREYYRKLGYERDGPYMSKDL 432
Radical_SAM_C pfam16199
Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of ...
315-392 3.59e-24

Radical_SAM C-terminal domain; This domain is found as a C-terminal extension to a subset of Radical_SAM domains. It is found in archaeal, bacterial, fungal, plant and human proteins.


Pssm-ID: 465061 [Multi-domain]  Cd Length: 83  Bit Score: 96.31  E-value: 3.59e-24
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 19920684   315 DGLKIYPTLVIRGTGLYELWKTGRYKSYPPSMLVDLVAKILALVPPWTRVYRVQRDIPMPLVSSGVEHG-NLRELALAR 392
Cdd:pfam16199   2 DGVKIHPLLVLKGTPLAELYERGEYKPLSLEEYVELVADFLELLPPDIVIHRLGGDAPKELLVAPPWHLpKFRVLNLVE 80
Elp3 smart00729
Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, ...
91-351 7.81e-22

Elongator protein 3, MiaB family, Radical SAM; This superfamily contains MoaA, NifB, PqqE, coproporphyrinogen III oxidase, biotin synthase and MiaB families, and includes a representative in the eukaryotic elongator subunit, Elp-3. Some members of the family are methyltransferases.


Pssm-ID: 214792 [Multi-domain]  Cd Length: 216  Bit Score: 94.01  E-value: 7.81e-22
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684     91 VVAVMCKPHRCPHInmtgniCVYCpggpdsdfeystqsytgYEPTSMRAIRSRYdpfLQTRHR-VEQLKQLGHSVDKVEF 169
Cdd:smart00729   1 PLALYIITRGCPRR------CTFC-----------------SFPSLRGKLRSRY---LEALVReIELLAEKGEKEGLVGT 54
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    170 IVM-GGTFMCLPEEYRDYFIRNLHDalsghssanvaeavrysEKSRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIG 248
Cdd:smart00729  55 VFIgGGTPTLLSPEQLEELLEAIRE-----------------ILGLAKDVEITIETRPDTLTEELLEALKEAGVNRVSLG 117
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    249 VQSVYEDVARDTNRGHTVRAVCESFQLGKDAG-YKIVTHMMPDLPNVDFErDIEQFIEYFEnpAFRSDGLKIYPTLVIRG 327
Cdd:smart00729 118 VQSGDDEVLKAINRGHTVEDVLEAVELLREAGpIKVSTDLIVGLPGETEE-DFEETLKLLK--ELGPDRVSIFPLSPRPG 194
                          250       260
                   ....*....|....*....|....
gi 19920684    328 TGLYELWKtgRYKSYPPSMLVDLV 351
Cdd:smart00729 195 TPLAKMYK--RLKPPTKEERAELL 216
Radical_SAM cd01335
Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S ...
98-346 1.45e-12

Radical SAM superfamily. Enzymes of this family generate radicals by combining a 4Fe-4S cluster and S-adenosylmethionine (SAM) in close proximity. They are characterized by a conserved CxxxCxxC motif, which coordinates the conserved iron-sulfur cluster. Mechanistically, they share the transfer of a single electron from the iron-sulfur cluster to SAM, which leads to its reductive cleavage to methionine and a 5'-deoxyadenosyl radical, which, in turn, abstracts a hydrogen from the appropriately positioned carbon atom. Depending on the enzyme, SAM is consumed during this process or it is restored and reused. Radical SAM enzymes catalyze steps in metabolism, DNA repair, the biosynthesis of vitamins and coenzymes, and the biosynthesis of many antibiotics. Examples are biotin synthase (BioB), lipoyl synthase (LipA), pyruvate formate-lyase (PFL), coproporphyrinogen oxidase (HemN), lysine 2,3-aminomutase (LAM), anaerobic ribonucleotide reductase (ARR), and MoaA, an enzyme of the biosynthesis of molybdopterin.


Pssm-ID: 100105 [Multi-domain]  Cd Length: 204  Bit Score: 66.97  E-value: 1.45e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  98 PHRCPHInmtgniCVYCPGGPDSDFEYSTQSYTGYEptsmrairsrydpflqtRHRVEQLKQLGHSVdkveFIVMGGTfm 177
Cdd:cd01335   4 TRGCNLN------CGFCSNPASKGRGPESPPEIEEI-----------------LDIVLEAKERGVEV----VILTGGE-- 54
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 178 CLPEEYRDYFIRNLHDalsghssanvaeavryseksRTKCIGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVA 257
Cdd:cd01335  55 PLLYPELAELLRRLKK--------------------ELPGFEISIETNGTLLTEELLKELKELGLDGVGVSLDSGDEEVA 114
                       170       180       190       200       210       220       230       240
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 258 RDTN-RGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFERDIEQFIeyFENPAFRSDGLKIYPTLVIRGTGLYELWKT 336
Cdd:cd01335 115 DKIRgSGESFKERLEALKELREAGLGLSTTLLVGLGDEDEEDDLEELE--LLAEFRSPDRVSLFRLLPEEGTPLELAAPV 192
                       250
                ....*....|
gi 19920684 337 GRYKSYPPSM 346
Cdd:cd01335 193 VPAEKLLRLI 202
Radical_SAM pfam04055
Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual ...
99-303 7.73e-12

Radical SAM superfamily; Radical SAM proteins catalyze diverse reactions, including unusual methylations, isomerization, sulphur insertion, ring formation, anaerobic oxidation and protein radical formation.


Pssm-ID: 427681 [Multi-domain]  Cd Length: 159  Bit Score: 63.70  E-value: 7.73e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684    99 HRCPHInmtgniCVYCpggpdsdfeystqsytgYEPTSMRAIRSRYDPFLQTRHRVEQLKQLGhsvdKVEFIVMGGTFMC 178
Cdd:pfam04055   3 RGCNLR------CTYC-----------------AFPSIRARGKGRELSPEEILEEAKELKRLG----VEVVILGGGEPLL 55
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684   179 LPEEYRDYFIRNLHDALSGhssanvaeavryseksrtkcIGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVAR 258
Cdd:pfam04055  56 LPDLVELLERLLKLELAEG--------------------IRITLETNGTLLDEELLELLKEAGLDRVSIGLESGDDEVLK 115
                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*
gi 19920684   259 DTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFErDIEQF 303
Cdd:pfam04055 116 LINRGHTFEEVLEALELLREAGIPVVTDNIVGLPGETDE-DLEET 159
HemN COG0635
Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase ...
220-340 2.39e-07

Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase [Coenzyme transport and metabolism]; Coproporphyrinogen-III oxidase HemN (oxygen-independent) or related Fe-S oxidoreductase is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 440400 [Multi-domain]  Cd Length: 400  Bit Score: 53.26  E-value: 2.39e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 220 ITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVARDTNRGHTVRAVCESFQLGKDAGYKIVTHmmpDL----PN-- 293
Cdd:COG0635 111 ITLEANPGTVTAEKLAALREAGVNRLSLGVQSFDDEVLKALGRIHTAEEALAAVELAREAGFDNINL---DLiyglPGqt 187
                        90       100       110       120
                ....*....|....*....|....*....|....*....|....*....
gi 19920684 294 -VDFERDIEQFIEYfeNPafrsDGLKIYPtLVIR-GTGLYELWKTGRYK 340
Cdd:COG0635 188 lESWEETLEKALAL--GP----DHISLYS-LTHEpGTPFAQRVRRGKLA 229
YgiQ COG1032
Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];
218-338 2.78e-06

Radical SAM superfamily enzyme YgiQ, UPF0313 family [General function prediction only];


Pssm-ID: 440655 [Multi-domain]  Cd Length: 394  Bit Score: 49.56  E-value: 2.78e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 218 IGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVARDTNRGHTVRAVCESFQLGKDAGYKIVTHMMPDLPNVDFE 297
Cdd:COG1032 253 VSFPSEVRVDLLDEELLELLKKAGCRGLFIGIESGSQRVLKAMNKGITVEDILEAVRLLKKAGIRVKLYFIIGLPGETEE 332
                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 19920684 298 rDIEQFIEYFEnpAFRSDGLKIYPTLVIRGTGLYE-LWKTGR 338
Cdd:COG1032 333 -DIEETIEFIK--ELGPDQAQVSIFTPLPGTPLYEeLEKEGR 371
PRK08208 PRK08208
coproporphyrinogen III oxidase family protein;
218-399 2.45e-05

coproporphyrinogen III oxidase family protein;


Pssm-ID: 181292 [Multi-domain]  Cd Length: 430  Bit Score: 46.93  E-value: 2.45e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  218 IGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVARDTNRGHTVRAVCESFQLGKDAGYkivthmmPDLpNVD-- 295
Cdd:PRK08208 128 IPKSVETSPATTTAEKLALLAARGVNRLSIGVQSFHDSELHALHRPQKRADVHQALEWIRAAGF-------PIL-NIDli 199
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  296 ----------FERDIEQFIEYfenpafRSDGLKIYPTLVIRGTGLYElwktgRYKSYPPSMLvdlvakilalvppwtRVY 365
Cdd:PRK08208 200 ygipgqthasWMESLDQALVY------RPEELFLYPLYVRPLTGLGR-----RARAWDDQRL---------------SLY 253
                        170       180       190
                 ....*....|....*....|....*....|....
gi 19920684  366 RVQRDIpmpLVSSGVEHGNLRELALARMKDLGTT 399
Cdd:PRK08208 254 RLARDL---LLEAGYTQTSMRMFRRNDAPDKGAP 284
RaSEA COG1244
Archaeosine formation enzyme, radical SAM superfamily [Translation, ribosomal structure and ...
213-360 3.87e-04

Archaeosine formation enzyme, radical SAM superfamily [Translation, ribosomal structure and biogenesis];


Pssm-ID: 440857 [Multi-domain]  Cd Length: 346  Bit Score: 42.62  E-value: 3.87e-04
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 213 SRTKCIGITIETRPDYCLKRHISDMLSY-GCTRLE--IGVQSVYEDVARDT-NRGHT----VRAVcesfQLGKDAGYKIV 284
Cdd:COG1244 126 AEDGVKKVIVESRPEFVTEETLEEFREIlGGKRLEvaIGLETSNDEIREKCiNKGFTfkdfERAA----ELLKEAGIGVK 201
                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684 285 THMM---PDLPnvdfERD-IEQFIEYFENPAFRSDGLKIYPTLVIRGTGLYELWKTGRYKsyPPSM--LVDLVAKILALV 358
Cdd:COG1244 202 AYLLlkpPFLS----EKEaIEDAIRSVEDAAPYADTISLNPTNVQKGTLVERLWKRGEYR--PPWLwsVVEVLKEAKATV 275

                ..
gi 19920684 359 PP 360
Cdd:COG1244 276 DA 277
PRK05904 PRK05904
coproporphyrinogen III oxidase; Provisional
173-305 9.89e-04

coproporphyrinogen III oxidase; Provisional


Pssm-ID: 235641 [Multi-domain]  Cd Length: 353  Bit Score: 41.72  E-value: 9.89e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  173 GGTFMCLPEEYRDYFIRNLhdalsghssanvaeavrySEKSRTKCiGITIETRPDYCLKRHISDMLSYGCTRLEIGVQSV 252
Cdd:PRK05904  64 GGTPNCLNDQLLDILLSTI------------------KPYVDNNC-EFTIECNPELITQSQINLLKKNKVNRISLGVQSM 124
                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 19920684  253 YEDVARDTNRGHTVRAVCESFQLGKDAGYKIVT----HMMPDLPNVDFErDIEQFIE 305
Cdd:PRK05904 125 NNNILKQLNRTHTIQDSKEAINLLHKNGIYNIScdflYCLPILKLKDLD-EVFNFIL 180
PRK08207 PRK08207
coproporphyrinogen III oxidase; Provisional
111-340 1.35e-03

coproporphyrinogen III oxidase; Provisional


Pssm-ID: 236187 [Multi-domain]  Cd Length: 488  Bit Score: 41.40  E-value: 1.35e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  111 CVYCpggpdsdfeystqSYTGYEptsMRAIRSRYDPFLQTRHR-----VEQLKQLGHSVDKVEFivMGGTFMCLPEEYRD 185
Cdd:PRK08207 177 CLYC-------------SFPSYP---IKGYKGLVEPYLEALHYeieeiGKYLKEKGLKITTIYF--GGGTPTSLTAEELE 238
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  186 YFIRNLHDALSGHSsaNVAEavryseksrtkcigITIET-RPDYCLKRHISDMLSYGCTRLEIGVQSVYEDVARDTNRGH 264
Cdd:PRK08207 239 RLLEEIYENFPDVK--NVKE--------------FTVEAgRPDTITEEKLEVLKKYGVDRISINPQTMNDETLKAIGRHH 302
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 19920684  265 TVRAVCESFQLGKDAGYKIVtHMmpD----LPNVDfERDIEQFIEYFE--NPafrsDGLKIYpTLVI-RGTGLYELWKtg 337
Cdd:PRK08207 303 TVEDIIEKFHLAREMGFDNI-NM--DliigLPGEG-LEEVKHTLEEIEklNP----ESLTVH-TLAIkRASRLTENKE-- 371

                 ...
gi 19920684  338 RYK 340
Cdd:PRK08207 372 KYK 374
 
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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