RibD family protein (named after riboflavin biosynthesis protein RibD) is a reductase similar to Aquifex aeolicus 2,5-diamino-6-(ribosylamino)-4(3H)-pyrimidinone 5'-phosphate reductase RibD2 that catalyzes an early step in riboflavin biosynthesis, the NADPH-dependent reduction of the ribose side chain of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, yielding 2,5-diamino-6-ribitylamino-4(3H)-pyrimidinone 5'-phosphate
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine ...
16-216
6.33e-33
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine reductase, riboflavin biosynthesis is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis
:
Pssm-ID: 441588 Cd Length: 217 Bit Score: 119.49 E-value: 6.33e-33
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine ...
16-216
6.33e-33
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine reductase, riboflavin biosynthesis is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis
Pssm-ID: 441588 Cd Length: 217 Bit Score: 119.49 E-value: 6.33e-33
riboflavin-specific deaminase C-terminal domain; Eubacterial riboflavin-specific deaminases have a zinc-binding domain recognized by the dCMP_cyt_deam model toward the N-terminus and this domain toward the C-terminus. Yeast HTP reductase, a riboflavin-biosynthetic enzyme, and several archaeal proteins believed related to riboflavin biosynthesis consist only of this domain and lack the dCMP_cyt_deam domain.
Pssm-ID: 129330 [Multi-domain] Cd Length: 216 Bit Score: 98.23 E-value: 9.24e-25
RibD C-terminal domain; The function of this domain is not known, but it is thought to be ...
16-216
4.50e-21
RibD C-terminal domain; The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG, in combination with pfam00383, as well as in isolation in some archaebacterial proteins. This family appears to be related to pfam00186.
Pssm-ID: 396444 Cd Length: 196 Bit Score: 87.82 E-value: 4.50e-21
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine ...
16-216
6.33e-33
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine reductase, riboflavin biosynthesis is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis
Pssm-ID: 441588 Cd Length: 217 Bit Score: 119.49 E-value: 6.33e-33
riboflavin-specific deaminase C-terminal domain; Eubacterial riboflavin-specific deaminases have a zinc-binding domain recognized by the dCMP_cyt_deam model toward the N-terminus and this domain toward the C-terminus. Yeast HTP reductase, a riboflavin-biosynthetic enzyme, and several archaeal proteins believed related to riboflavin biosynthesis consist only of this domain and lack the dCMP_cyt_deam domain.
Pssm-ID: 129330 [Multi-domain] Cd Length: 216 Bit Score: 98.23 E-value: 9.24e-25
RibD C-terminal domain; The function of this domain is not known, but it is thought to be ...
16-216
4.50e-21
RibD C-terminal domain; The function of this domain is not known, but it is thought to be involved in riboflavin biosynthesis. This domain is found in the C terminus of RibD/RibG, in combination with pfam00383, as well as in isolation in some archaebacterial proteins. This family appears to be related to pfam00186.
Pssm-ID: 396444 Cd Length: 196 Bit Score: 87.82 E-value: 4.50e-21
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1'-reductase, archaeal; This model ...
16-216
4.35e-19
2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine 1'-reductase, archaeal; This model represents a specific reductase of riboflavin biosynthesis in the Archaea, diaminohydroxyphosphoribosylaminopyrimidine reductase. It should not be confused with bacterial 5-amino-6-(5-phosphoribosylamino)uracil reductase. The intermediate 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)pyrimidine in riboflavin biosynthesis is reduced first, and then deaminated, in both Archaea and Fungi, opposite the order in Bacteria. The subsequent deaminase is not presently known and is not closely homologous to the deaminase domain (3.5.4.26) fused to the reductase domain (1.1.1.193) similar to this protein but found in most bacteria.
Pssm-ID: 130572 Cd Length: 210 Bit Score: 82.93 E-value: 4.35e-19
riboflavin biosynthesis protein RibD; This model describes the ribD protein as found in ...
17-220
3.22e-12
riboflavin biosynthesis protein RibD; This model describes the ribD protein as found in Escherichia coli. The N-terminal domain includes the conserved zinc-binding site region captured in the model dCMP_cyt_deam and shared by proteins such as cytosine deaminase, mammalian apolipoprotein B mRNA editing protein, blasticidin-S deaminase, and Bacillus subtilis competence protein comEB. The C-terminal domain is homologous to the full length of yeast HTP reductase, a protein required for riboflavin biosynthesis. A number of archaeal proteins believed related to riboflavin biosynthesis contain only this C-terminal domain and are not found as full-length matches to this model. [Biosynthesis of cofactors, prosthetic groups, and carriers, Riboflavin, FMN, and FAD]
Pssm-ID: 273015 [Multi-domain] Cd Length: 344 Bit Score: 65.62 E-value: 3.22e-12
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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