NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1190332491|ref|NP_001338308|]
View 

enhancer of mRNA-decapping protein 3 isoform 2 [Homo sapiens]

Protein Classification

LSM14 family protein; bifunctional ADP-dependent NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase( domain architecture ID 11072268)

LSM14 family protein having an Sm fold consisting of a five-stranded beta-sheet and an alpha-helix at the N-terminus, may be involved in essential RNA-processing tasks; bifunctional ADP-dependent NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase catalyzes the epimerization of the S- and R-forms of NAD(P)HX and the dehydration of the S-form of NAD(P)HX at the expense of ADP, allowing the repair of both epimers of NAD(P)HX

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
Edc3_linker super family cl24976
Linker region of enhancer of mRNA-decapping protein 3; This region is located between the ...
 1-49 1.08e-33

Linker region of enhancer of mRNA-decapping protein 3; This region is located between the LSM14 pfam12701 (Lsm) and FDF pfam09532 domains of the enhancer of mRNA-decapping protein 3. This region is predicted to be natively unstructured. Its precise functional role is not known.


The actual alignment was detected with superfamily member pfam16598:

Pssm-ID: 465188  Cd Length: 91  Bit Score: 120.08  E-value: 1.08e-33
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1190332491   1 MESLSQSKSFRRRHNSWSSSSRHPNQATPKKSGLKNGQMKNKDDECFGD 49
Cdd:pfam16598  43 LDSLGQSKGFRRRHNSWSSSSRGPNQATPKKNGVKNGQMKSKDDECFGD 91
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 53-156 3.19e-31

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


:

Pssm-ID: 430668  Cd Length: 104  Bit Score: 114.09  E-value: 3.19e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491  53 EIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNeRPTRYRHDENILESEPIVYRRIIVPHNVSKEFCTDSGL 132
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNEN-NATRVATNEQPNEEVKGVYKKDDFFDNISSEANDRGIQ 79

                          90       100
                  ....*....|....*....|....*
gi 1190332491 133 VVPSISYELHKKLLSV-AEKHGLTL 156
Cdd:pfam09532  80 SGPSPSGRDWREERSLnTETFGVDS 104
YjeF_N pfam03853
YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a ...
 157-310 2.29e-22

YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions.


:

Pssm-ID: 427546 [Multi-domain]  Cd Length: 168  Bit Score: 92.29  E-value: 2.29e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 157 ERRLEMTGVCASQMALTLLggpnrlnpknVHQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITN 235
Cdd:pfam03853   2 AVLMENAGRAAARVLKALL----------SPAGPKVLILCGPGNNGGDGLAAARHLANRGAKVTVLlLGPEEKLSEDARR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 236 ELSLFSKTQGQ----QVSSLKDLPTSPVDLVINCLDcpeNVFLR--DQPWYKAAVAWANQNRAPVLSIDPPVheveqGID 309
Cdd:pfam03853  72 QLDLFKKLGGKivtdNPDEDLEKLLSPVDLIIDALL---GTGLSgpLRGEYAALIEWINQSGAPVLAVDIPS-----GLD 143


                  .
gi 1190332491 310 A 310
Cdd:pfam03853 144 A 144
 
Name Accession Description Interval E-value
Edc3_linker pfam16598
Linker region of enhancer of mRNA-decapping protein 3; This region is located between the ...
 1-49 1.08e-33

Linker region of enhancer of mRNA-decapping protein 3; This region is located between the LSM14 pfam12701 (Lsm) and FDF pfam09532 domains of the enhancer of mRNA-decapping protein 3. This region is predicted to be natively unstructured. Its precise functional role is not known.


Pssm-ID: 465188  Cd Length: 91  Bit Score: 120.08  E-value: 1.08e-33
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1190332491   1 MESLSQSKSFRRRHNSWSSSSRHPNQATPKKSGLKNGQMKNKDDECFGD 49
Cdd:pfam16598  43 LDSLGQSKGFRRRHNSWSSSSRGPNQATPKKNGVKNGQMKSKDDECFGD 91
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 53-156 3.19e-31

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


Pssm-ID: 430668  Cd Length: 104  Bit Score: 114.09  E-value: 3.19e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491  53 EIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNeRPTRYRHDENILESEPIVYRRIIVPHNVSKEFCTDSGL 132
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNEN-NATRVATNEQPNEEVKGVYKKDDFFDNISSEANDRGIQ 79

                          90       100
                  ....*....|....*....|....*
gi 1190332491 133 VVPSISYELHKKLLSV-AEKHGLTL 156
Cdd:pfam09532  80 SGPSPSGRDWREERSLnTETFGVDS 104
YjeF_N pfam03853
YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a ...
 157-310 2.29e-22

YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions.


Pssm-ID: 427546 [Multi-domain]  Cd Length: 168  Bit Score: 92.29  E-value: 2.29e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 157 ERRLEMTGVCASQMALTLLggpnrlnpknVHQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITN 235
Cdd:pfam03853   2 AVLMENAGRAAARVLKALL----------SPAGPKVLILCGPGNNGGDGLAAARHLANRGAKVTVLlLGPEEKLSEDARR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 236 ELSLFSKTQGQ----QVSSLKDLPTSPVDLVINCLDcpeNVFLR--DQPWYKAAVAWANQNRAPVLSIDPPVheveqGID 309
Cdd:pfam03853  72 QLDLFKKLGGKivtdNPDEDLEKLLSPVDLIIDALL---GTGLSgpLRGEYAALIEWINQSGAPVLAVDIPS-----GLD 143


                  .
gi 1190332491 310 A 310
Cdd:pfam03853 144 A 144
Nnr1 COG0062
NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and ...
 187-298 1.66e-05

NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and metabolism];


Pssm-ID: 439832 [Multi-domain]  Cd Length: 499  Bit Score: 46.40  E-value: 1.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 187 HQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILFLPNFVKML--ESITNeLSLFsKTQGQQVSSLKDLPTSP--VDLV 262
Cdd:COG0062    45 SAARRVLVLCGPGNNGGDGLVAARLLAEAGYNVTVFLLGDPEKLsgDAAAN-LERL-KAAGIPILELDDELPELaeADLI 122

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1190332491 263 INCLdcpenvF-------LRDqpWYKAAVAWANQNRAPVLSID 298
Cdd:COG0062   123 VDAL------FgtglsrpLRG--PYAELIEAINASGAPVLAVD 157
PLN03050 PLN03050
pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional
 140-220 1.37e-04

pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional


Pssm-ID: 215551 [Multi-domain]  Cd Length: 246  Bit Score: 42.94  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 140 ELHKKLLSVAekhGLTLERRLEMTGVCASQMALTLLGGPNRLNPKNVHQRptVALLCGPHVKGAQGISCGRHLAN--HDV 217
Cdd:PLN03050   16 ALDEELMSTP---GFSLEQLMELAGLSVAEAVYEVADGEKASNPPGRHPR--VLLVCGPGNNGGDGLVAARHLAHfgYEV 90


                  ...
gi 1190332491 218 QVI 220
Cdd:PLN03050   91 TVC 93
yjeF_nterm TIGR00197
yjeF N-terminal region; The protein region corresponding to this model shows no clear homology ...
 189-337 7.27e-03

yjeF N-terminal region; The protein region corresponding to this model shows no clear homology to any protein of known function. This model is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO match the yjeF C-terminal domain but lack this region. [Unknown function, General]


Pssm-ID: 272956 [Multi-domain]  Cd Length: 205  Bit Score: 37.39  E-value: 7.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 189 RPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITNELSLFSKTQGQQVSSLKDLPTSpVDLVInclD 267
Cdd:TIGR00197  45 AGHVIIFCGPGNNGGDGFVVARHLKGFGVEVFLLkKEKRIECTEQAEVNLKALKVGGISIDEGNLVKPED-CDVII---D 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 268 CPENVFLRDQPW--YKAAVAWANQNRAPVLSIDPPvheveQGIDAKWSLALGL-----------------PLPLGEHAGR 328
Cdd:TIGR00197 121 AILGTGFKGKLRepFKTIVESINELPAPIVSVDIP-----SGLDVDTGAIEGPavnadltitfhaikpclLSDRADVTGE 195


                  ....*....
gi 1190332491 329 IYLCDIGIP 337
Cdd:TIGR00197 196 LKVGGIGIP 204
 
Name Accession Description Interval E-value
Edc3_linker pfam16598
Linker region of enhancer of mRNA-decapping protein 3; This region is located between the ...
 1-49 1.08e-33

Linker region of enhancer of mRNA-decapping protein 3; This region is located between the LSM14 pfam12701 (Lsm) and FDF pfam09532 domains of the enhancer of mRNA-decapping protein 3. This region is predicted to be natively unstructured. Its precise functional role is not known.


Pssm-ID: 465188  Cd Length: 91  Bit Score: 120.08  E-value: 1.08e-33
                          10        20        30        40
                  ....*....|....*....|....*....|....*....|....*....
gi 1190332491   1 MESLSQSKSFRRRHNSWSSSSRHPNQATPKKSGLKNGQMKNKDDECFGD 49
Cdd:pfam16598  43 LDSLGQSKGFRRRHNSWSSSSRGPNQATPKKNGVKNGQMKSKDDECFGD 91
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 53-156 3.19e-31

FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an entirely alpha-helical domain with multiple exposed hydrophilic loops. It is found at the C terminus of Scd6p-like SM domains. It is also found with other divergent Sm domains and in proteins such as Dcp3p and FLJ21128, where it is found N terminal to the YjeF-N domain, a novel Rossmann fold domain.


Pssm-ID: 430668  Cd Length: 104  Bit Score: 114.09  E-value: 3.19e-31
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491  53 EIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNeRPTRYRHDENILESEPIVYRRIIVPHNVSKEFCTDSGL 132
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNEN-NATRVATNEQPNEEVKGVYKKDDFFDNISSEANDRGIQ 79

                          90       100
                  ....*....|....*....|....*
gi 1190332491 133 VVPSISYELHKKLLSV-AEKHGLTL 156
Cdd:pfam09532  80 SGPSPSGRDWREERSLnTETFGVDS 104
YjeF_N pfam03853
YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a ...
 157-310 2.29e-22

YjeF-related protein N-terminus; YjeF-N domain is a novel version of the Rossmann fold with a set of catalytic residues and structural features that are different from the conventional dehydrogenases. YjeF-N domain is fused to Ribokinases in bacteria (YjeF), where they may be phosphatases, and to divergent Sm and the FDF domain in eukaryotes (Dcp3p and FLJ21128), where they may be involved in decapping and catalyze hydrolytic RNA-processing reactions.


Pssm-ID: 427546 [Multi-domain]  Cd Length: 168  Bit Score: 92.29  E-value: 2.29e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 157 ERRLEMTGVCASQMALTLLggpnrlnpknVHQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITN 235
Cdd:pfam03853   2 AVLMENAGRAAARVLKALL----------SPAGPKVLILCGPGNNGGDGLAAARHLANRGAKVTVLlLGPEEKLSEDARR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 236 ELSLFSKTQGQ----QVSSLKDLPTSPVDLVINCLDcpeNVFLR--DQPWYKAAVAWANQNRAPVLSIDPPVheveqGID 309
Cdd:pfam03853  72 QLDLFKKLGGKivtdNPDEDLEKLLSPVDLIIDALL---GTGLSgpLRGEYAALIEWINQSGAPVLAVDIPS-----GLD 143


                  .
gi 1190332491 310 A 310
Cdd:pfam03853 144 A 144
Nnr1 COG0062
NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and ...
 187-298 1.66e-05

NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and metabolism];


Pssm-ID: 439832 [Multi-domain]  Cd Length: 499  Bit Score: 46.40  E-value: 1.66e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 187 HQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILFLPNFVKML--ESITNeLSLFsKTQGQQVSSLKDLPTSP--VDLV 262
Cdd:COG0062    45 SAARRVLVLCGPGNNGGDGLVAARLLAEAGYNVTVFLLGDPEKLsgDAAAN-LERL-KAAGIPILELDDELPELaeADLI 122

                          90       100       110       120
                  ....*....|....*....|....*....|....*....|...
gi 1190332491 263 INCLdcpenvF-------LRDqpWYKAAVAWANQNRAPVLSID 298
Cdd:COG0062   123 VDAL------FgtglsrpLRG--PYAELIEAINASGAPVLAVD 157
PLN03050 PLN03050
pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional
 140-220 1.37e-04

pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional


Pssm-ID: 215551 [Multi-domain]  Cd Length: 246  Bit Score: 42.94  E-value: 1.37e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 140 ELHKKLLSVAekhGLTLERRLEMTGVCASQMALTLLGGPNRLNPKNVHQRptVALLCGPHVKGAQGISCGRHLAN--HDV 217
Cdd:PLN03050   16 ALDEELMSTP---GFSLEQLMELAGLSVAEAVYEVADGEKASNPPGRHPR--VLLVCGPGNNGGDGLVAARHLAHfgYEV 90


                  ...
gi 1190332491 218 QVI 220
Cdd:PLN03050   91 TVC 93
yjeF_nterm TIGR00197
yjeF N-terminal region; The protein region corresponding to this model shows no clear homology ...
 189-337 7.27e-03

yjeF N-terminal region; The protein region corresponding to this model shows no clear homology to any protein of known function. This model is built on yeast protein YNL200C and the N-terminal regions of E. coli yjeF and its orthologs in various species. The C-terminal region of yjeF and its orthologs shows similarity to hydroxyethylthiazole kinase (thiM) and other enzymes involved in thiamine biosynthesis. Yeast YKL151C and B. subtilis yxkO match the yjeF C-terminal domain but lack this region. [Unknown function, General]


Pssm-ID: 272956 [Multi-domain]  Cd Length: 205  Bit Score: 37.39  E-value: 7.27e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 189 RPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITNELSLFSKTQGQQVSSLKDLPTSpVDLVInclD 267
Cdd:TIGR00197  45 AGHVIIFCGPGNNGGDGFVVARHLKGFGVEVFLLkKEKRIECTEQAEVNLKALKVGGISIDEGNLVKPED-CDVII---D 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1190332491 268 CPENVFLRDQPW--YKAAVAWANQNRAPVLSIDPPvheveQGIDAKWSLALGL-----------------PLPLGEHAGR 328
Cdd:TIGR00197 121 AILGTGFKGKLRepFKTIVESINELPAPIVSVDIP-----SGLDVDTGAIEGPavnadltitfhaikpclLSDRADVTGE 195


                  ....*....
gi 1190332491 329 IYLCDIGIP 337
Cdd:TIGR00197 196 LKVGGIGIP 204
 
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.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH