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Conserved domains on  [gi|1545705898|gb|RUN52578|]
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5'(3')-deoxyribonucleotidase [Staphylococcus epidermidis]

Protein Classification

YorC family protein( domain architecture ID 10008597)

YorC family protein

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
2-177 1.24e-81

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


:

Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 239.39  E-value: 1.24e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   2 TRERIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMI-PEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQL 80
Cdd:COG4502     1 MKPRIAVDMDGVLADFYAAFLDIYNKEYGTNLTLEDLDGWDLWELVpPEHRERIREFLNEPGFFRDLPPIPGAQEVLKEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  81 NEYYDIYIATAAMDVPTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVNEHR 160
Cdd:COG4502    81 SDKYEVYIVTAAMEFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNPKNLEEFKGKGILFDAPHNRHITG 160

                         170
                  ....*....|....*..
gi 1545705898 161 FERVSGWRDVKNYFNSI 177
Cdd:COG4502   161 YPRVNNWKEVEALLLSL 177
 
Name Accession Description Interval E-value
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
2-177 1.24e-81

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 239.39  E-value: 1.24e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   2 TRERIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMI-PEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQL 80
Cdd:COG4502     1 MKPRIAVDMDGVLADFYAAFLDIYNKEYGTNLTLEDLDGWDLWELVpPEHRERIREFLNEPGFFRDLPPIPGAQEVLKEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  81 NEYYDIYIATAAMDVPTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVNEHR 160
Cdd:COG4502    81 SDKYEVYIVTAAMEFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNPKNLEEFKGKGILFDAPHNRHITG 160

                         170
                  ....*....|....*..
gi 1545705898 161 FERVSGWRDVKNYFNSI 177
Cdd:COG4502   161 YPRVNNWKEVEALLLSL 177
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 5-155 2.25e-59

5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319786  Cd Length: 161  Bit Score: 182.20  E-value: 2.25e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   5 RIAIDMDEVLADTLGAVVKAVNERAD------LNIKMESLNGKKLKHmiPEHEGLVMDILKEPGFFRNLDVMPHAQEVVK 78
Cdd:cd02587     2 VILVDMDGVLADFEGALVRAIRERFPdephvlLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  79 QLN-EYYDIYIATAAMDV-PTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEG---KSIMFTAS 153
Cdd:cd02587    80 ELSdEGTDVYICTSPLNKyPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGpgwEHILFTAC 159


                  ..
gi 1545705898 154 HN 155
Cdd:cd02587   160 HN 161
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 3-170 3.31e-36

5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known.


Pssm-ID: 284381 [Multi-domain]  Cd Length: 180  Bit Score: 123.87  E-value: 3.31e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   3 RERIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMI-PEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQL- 80
Cdd:pfam06941   1 RSIIGVDLDGVCADFYGRMRQIANEWFERPLLPEEVSSWGWSEWTnPEQYDSLHRFVTQPGFFSDLEPIPGAREYLRQLs 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  81 NEYYDIYIATAAMDVPTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVNEHR 160
Cdd:pfam06941  81 DEGRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPENLAQLRGRGILFGNPTNRHIED 160

                         170
                  ....*....|
gi 1545705898 161 FERVSGWRDV 170
Cdd:pfam06941 161 ELRAASWQEV 170
 
Name Accession Description Interval E-value
YorC COG4502
5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];
2-177 1.24e-81

5'(3')-deoxyribonucleotidase [Nucleotide transport and metabolism];


Pssm-ID: 443586 [Multi-domain]  Cd Length: 177  Bit Score: 239.39  E-value: 1.24e-81
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   2 TRERIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMI-PEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQL 80
Cdd:COG4502     1 MKPRIAVDMDGVLADFYAAFLDIYNKEYGTNLTLEDLDGWDLWELVpPEHRERIREFLNEPGFFRDLPPIPGAQEVLKEL 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  81 NEYYDIYIATAAMDVPTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVNEHR 160
Cdd:COG4502    81 SDKYEVYIVTAAMEFPNSLEEKYEWLDEHFPFIPWQNIIFCGDKSLVGGDYLIDDNPKNLEEFKGKGILFDAPHNRHITG 160

                         170
                  ....*....|....*..
gi 1545705898 161 FERVSGWRDVKNYFNSI 177
Cdd:COG4502   161 YPRVNNWKEVEALLLSL 177
HAD_5-3dNT cd02587
5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) ...
 5-155 2.25e-59

5'(3')-deoxyribonucleotidase; This family includes cytosolic 5'(3')-deoxyribonucleotidase (cdN) and mitochondrial 5'(3')-deoxyribonucleotidase (mdN). cdN and mdN specifically dephosphorylate the deoxyribo form of nucleoside monophosphates helps maintain homeostasis of deoxynucleosides required for mitochondrial DNA synthesis. Their preferred substrates are dUMP and dTMP. cdN also dephosphorylates dGMP and dIMP efficiently. They can also dephosphorylate the 5'- or 3'-phosphates of pyrimidine ribonucleotides. This family belongs to the haloacid dehalogenase-like (HAD) hydrolases, a large superfamily of diverse enzymes that catalyze carbon or phosphoryl group transfer reactions on a range of substrates, using an active site aspartate in nucleophilic catalysis. Members of this superfamily include 2-L-haloalkanoic acid dehalogenase, azetidine hydrolase, phosphonoacetaldehyde hydrolase, phosphoserine phosphatase, phosphomannomutase, P-type ATPases and many others. HAD hydrolases are found in all three kingdoms of life, and most genomes are predicted to contain multiple HAD-like proteins. Members possess a highly conserved alpha/beta core domain, and many also possess a small cap domain, the fold and function of which is variable. HAD hydrolases are sometimes referred to as belonging to the DDDD superfamily of phosphohydrolases.


Pssm-ID: 319786  Cd Length: 161  Bit Score: 182.20  E-value: 2.25e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   5 RIAIDMDEVLADTLGAVVKAVNERAD------LNIKMESLNGKKLKHmiPEHEGLVMDILKEPGFFRNLDVMPHAQEVVK 78
Cdd:cd02587     2 VILVDMDGVLADFEGALVRAIRERFPdephvlLESRRGFWVIEQYKA--PELSRKAADILEEPGFFRNLEPIPGAVEALR 79

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  79 QLN-EYYDIYIATAAMDV-PTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEG---KSIMFTAS 153
Cdd:cd02587    80 ELSdEGTDVYICTSPLNKyPTCVEEKYEWVEEHFPPLFYQRIVLTRDKTVVLADILIDDNPENLEAFEGpgwEHILFTAC 159


                  ..
gi 1545705898 154 HN 155
Cdd:cd02587   160 HN 161
NT5C pfam06941
5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of ...
 3-170 3.31e-36

5' nucleotidase, deoxy (Pyrimidine), cytosolic type C protein (NT5C); This family consists of several 5' nucleotidase, deoxy (Pyrimidine), cytosolic type C (NT5C) proteins. 5'(3')-Deoxyribonucleotidase is a ubiquitous enzyme in mammalian cells whose physiological function is not known.


Pssm-ID: 284381 [Multi-domain]  Cd Length: 180  Bit Score: 123.87  E-value: 3.31e-36
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898   3 RERIAIDMDEVLADTLGAVVKAVNERADLNIKMESLNGKKLKHMI-PEHEGLVMDILKEPGFFRNLDVMPHAQEVVKQL- 80
Cdd:pfam06941   1 RSIIGVDLDGVCADFYGRMRQIANEWFERPLLPEEVSSWGWSEWTnPEQYDSLHRFVTQPGFFSDLEPIPGAREYLRQLs 80

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1545705898  81 NEYYDIYIATAAMDVPTSFHDKYEWLLEFFPFLDPQHFVFCGRKNIILADYLIDDNPKQLEIFEGKSIMFTASHNVNEHR 160
Cdd:pfam06941  81 DEGRIVIITHRLFQHYTAVQQKVNWLDSHLPGIPYWNLCFVKEKTQVRGDIYIDDSPENLAQLRGRGILFGNPTNRHIED 160

                         170
                  ....*....|
gi 1545705898 161 FERVSGWRDV 170
Cdd:pfam06941 161 ELRAASWQEV 170
 
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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