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Conserved domains on  [gi|767985465|ref|XP_011520394|]
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enhancer of mRNA-decapping protein 3 isoform X2 [Homo sapiens]

Protein Classification

LSM14 family protein; bifunctional ADP-dependent NAD(P)H-hydrate dehydratase/NAD(P)H-hydrate epimerase( domain architecture ID 10560091)

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

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List of domain hits

 Name Accession Description Interval E-value
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 15-118 4.99e-32

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: 115.24  E-value: 4.99e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465   15 EIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNeRPTRYRHDENILESEPIVYRRIIVPHNVSKEFCTDSGL 94
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNEN-NATRVATNEQPNEEVKGVYKKDDFFDNISSEANDRGIQ 79

                          90       100
                  ....*....|....*....|....*
gi 767985465   95 VVPSISYELHKKLLSV-AEKHGLTL 118
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 ...
 119-272 1.33e-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: 1.33e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  119 ERRLEMTGVCASQMALTLLggpnrlnpknVHQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITN 197
Cdd:pfam03853   2 AVLMENAGRAAARVLKALL----------SPAGPKVLILCGPGNNGGDGLAAARHLANRGAKVTVLlLGPEEKLSEDARR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  198 ELSLFSKTQGQ----QVSSLKDLPTSPVDLVINCLDcpeNVFLR--DQPWYKAAVAWANQNRAPVLSIDPPVheveqGID 271
Cdd:pfam03853  72 QLDLFKKLGGKivtdNPDEDLEKLLSPVDLIIDALL---GTGLSgpLRGEYAALIEWINQSGAPVLAVDIPS-----GLD 143


                  .
gi 767985465  272 A 272
Cdd:pfam03853 144 A 144
 
Name Accession Description Interval E-value
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 15-118 4.99e-32

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: 115.24  E-value: 4.99e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465   15 EIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNeRPTRYRHDENILESEPIVYRRIIVPHNVSKEFCTDSGL 94
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNEN-NATRVATNEQPNEEVKGVYKKDDFFDNISSEANDRGIQ 79

                          90       100
                  ....*....|....*....|....*
gi 767985465   95 VVPSISYELHKKLLSV-AEKHGLTL 118
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 ...
 119-272 1.33e-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: 1.33e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  119 ERRLEMTGVCASQMALTLLggpnrlnpknVHQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITN 197
Cdd:pfam03853   2 AVLMENAGRAAARVLKALL----------SPAGPKVLILCGPGNNGGDGLAAARHLANRGAKVTVLlLGPEEKLSEDARR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  198 ELSLFSKTQGQ----QVSSLKDLPTSPVDLVINCLDcpeNVFLR--DQPWYKAAVAWANQNRAPVLSIDPPVheveqGID 271
Cdd:pfam03853  72 QLDLFKKLGGKivtdNPDEDLEKLLSPVDLIIDALL---GTGLSgpLRGEYAALIEWINQSGAPVLAVDIPS-----GLD 143


                  .
gi 767985465  272 A 272
Cdd:pfam03853 144 A 144
Nnr1 COG0062
NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and ...
 149-260 1.33e-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: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465 149 HQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILFLPNFVKML--ESITNeLSLFsKTQGQQVSSLKDLPTSP--VDLV 224
Cdd:COG0062   45 SAARRVLVLCGPGNNGGDGLVAARLLAEAGYNVTVFLLGDPEKLsgDAAAN-LERL-KAAGIPILELDDELPELaeADLI 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 767985465 225 INCLdcpenvF-------LRDqpWYKAAVAWANQNRAPVLSID 260
Cdd:COG0062  123 VDAL------FgtglsrpLRG--PYAELIEAINASGAPVLAVD 157
PLN03050 PLN03050
pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional
 102-182 1.15e-04

pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional


Pssm-ID: 215551 [Multi-domain]  Cd Length: 246  Bit Score: 42.94  E-value: 1.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465 102 ELHKKLLSVAekhGLTLERRLEMTGVCASQMALTLLGGPNRLNPKNVHQRptVALLCGPHVKGAQGISCGRHLAN--HDV 179
Cdd:PLN03050  16 ALDEELMSTP---GFSLEQLMELAGLSVAEAVYEVADGEKASNPPGRHPR--VLLVCGPGNNGGDGLVAARHLAHfgYEV 90


                 ...
gi 767985465 180 QVI 182
Cdd:PLN03050  91 TVC 93
yjeF_nterm TIGR00197
yjeF N-terminal region; The protein region corresponding to this model shows no clear homology ...
 151-299 8.65e-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: 37.01  E-value: 8.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  151 RPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITNELSLFSKTQGQQVSSLKDLPTSpVDLVInclD 229
Cdd:TIGR00197  45 AGHVIIFCGPGNNGGDGFVVARHLKGFGVEVFLLkKEKRIECTEQAEVNLKALKVGGISIDEGNLVKPED-CDVII---D 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  230 CPENVFLRDQPW--YKAAVAWANQNRAPVLSIDPPvheveQGIDAKWSLALGL-----------------PLPLGEHAGR 290
Cdd:TIGR00197 121 AILGTGFKGKLRepFKTIVESINELPAPIVSVDIP-----SGLDVDTGAIEGPavnadltitfhaikpclLSDRADVTGE 195


                  ....*....
gi 767985465  291 IYLCDIGIP 299
Cdd:TIGR00197 196 LKVGGIGIP 204
 
Name Accession Description Interval E-value
FDF pfam09532
FDF domain; The FDF domain, so called because of the conserved FDF at its N termini, is an ...
 15-118 4.99e-32

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: 115.24  E-value: 4.99e-32
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465   15 EIPDTDFDFEGNLALFDKAAVFEEIDTYERRSGTRSRGIPNeRPTRYRHDENILESEPIVYRRIIVPHNVSKEFCTDSGL 94
Cdd:pfam09532   1 IKFDEDFDFESNNAKFNKQEVFAELRKNDKLDEEKRLVNEN-NATRVATNEQPNEEVKGVYKKDDFFDNISSEANDRGIQ 79

                          90       100
                  ....*....|....*....|....*
gi 767985465   95 VVPSISYELHKKLLSV-AEKHGLTL 118
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 ...
 119-272 1.33e-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: 1.33e-22
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  119 ERRLEMTGVCASQMALTLLggpnrlnpknVHQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITN 197
Cdd:pfam03853   2 AVLMENAGRAAARVLKALL----------SPAGPKVLILCGPGNNGGDGLAAARHLANRGAKVTVLlLGPEEKLSEDARR 71

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  198 ELSLFSKTQGQ----QVSSLKDLPTSPVDLVINCLDcpeNVFLR--DQPWYKAAVAWANQNRAPVLSIDPPVheveqGID 271
Cdd:pfam03853  72 QLDLFKKLGGKivtdNPDEDLEKLLSPVDLIIDALL---GTGLSgpLRGEYAALIEWINQSGAPVLAVDIPS-----GLD 143


                  .
gi 767985465  272 A 272
Cdd:pfam03853 144 A 144
Nnr1 COG0062
NAD(P)H-hydrate repair enzyme Nnr, NAD(P)H-hydrate epimerase domain [Nucleotide transport and ...
 149-260 1.33e-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: 1.33e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465 149 HQRPTVALLCGPHVKGAQGISCGRHLANHDVQVILFLPNFVKML--ESITNeLSLFsKTQGQQVSSLKDLPTSP--VDLV 224
Cdd:COG0062   45 SAARRVLVLCGPGNNGGDGLVAARLLAEAGYNVTVFLLGDPEKLsgDAAAN-LERL-KAAGIPILELDDELPELaeADLI 122

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|...
gi 767985465 225 INCLdcpenvF-------LRDqpWYKAAVAWANQNRAPVLSID 260
Cdd:COG0062  123 VDAL------FgtglsrpLRG--PYAELIEAINASGAPVLAVD 157
PLN03050 PLN03050
pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional
 102-182 1.15e-04

pyridoxine (pyridoxamine) 5'-phosphate oxidase; Provisional


Pssm-ID: 215551 [Multi-domain]  Cd Length: 246  Bit Score: 42.94  E-value: 1.15e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465 102 ELHKKLLSVAekhGLTLERRLEMTGVCASQMALTLLGGPNRLNPKNVHQRptVALLCGPHVKGAQGISCGRHLAN--HDV 179
Cdd:PLN03050  16 ALDEELMSTP---GFSLEQLMELAGLSVAEAVYEVADGEKASNPPGRHPR--VLLVCGPGNNGGDGLVAARHLAHfgYEV 90


                 ...
gi 767985465 180 QVI 182
Cdd:PLN03050  91 TVC 93
yjeF_nterm TIGR00197
yjeF N-terminal region; The protein region corresponding to this model shows no clear homology ...
 151-299 8.65e-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: 37.01  E-value: 8.65e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  151 RPTVALLCGPHVKGAQGISCGRHLANHDVQVILF-LPNFVKMLESITNELSLFSKTQGQQVSSLKDLPTSpVDLVInclD 229
Cdd:TIGR00197  45 AGHVIIFCGPGNNGGDGFVVARHLKGFGVEVFLLkKEKRIECTEQAEVNLKALKVGGISIDEGNLVKPED-CDVII---D 120

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 767985465  230 CPENVFLRDQPW--YKAAVAWANQNRAPVLSIDPPvheveQGIDAKWSLALGL-----------------PLPLGEHAGR 290
Cdd:TIGR00197 121 AILGTGFKGKLRepFKTIVESINELPAPIVSVDIP-----SGLDVDTGAIEGPavnadltitfhaikpclLSDRADVTGE 195


                  ....*....
gi 767985465  291 IYLCDIGIP 299
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.
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