Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with ...
69-418
5.27e-86
Dihydrofolate reductase (DHFR). Reduces 7,8-dihydrofolate to 5,6,7,8-tetrahydrofolate with NADPH as a cofactor. This is an essential step in the biosynthesis of deoxythymidine phosphate since 5,6,7,8-tetrahydrofolate is required to regenerate 5,10-methylenetetrahydrofolate which is then utilized by thymidylate synthase. Inhibition of DHFR interrupts thymidilate synthesis and DNA replication, inhibitors of DHFR (such as Methotrexate) are used in cancer chemotherapy. 5,6,7,8-tetrahydrofolate also is involved in glycine, serine, and threonine metabolism and aminoacyl-tRNA biosynthesis.
The actual alignment was detected with superfamily member TIGR00326:
Pssm-ID: 473077 [Multi-domain] Cd Length: 344 Bit Score: 272.09 E-value: 5.27e-86
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that ...
454-608
1.67e-68
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.
:
Pssm-ID: 274144 Cd Length: 153 Bit Score: 219.56 E-value: 1.67e-68
riboflavin biosynthesis protein RibD; This model describes the ribD protein as found in ...
69-418
5.27e-86
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: 272.09 E-value: 5.27e-86
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that ...
454-608
1.67e-68
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.
Pssm-ID: 274144 Cd Length: 153 Bit Score: 219.56 E-value: 1.67e-68
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine ...
214-418
3.88e-66
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: 215.41 E-value: 3.88e-66
Escherichia coli swarming motility protein YbiA and related proteins; This family of ...
452-606
8.96e-61
Escherichia coli swarming motility protein YbiA and related proteins; This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives, and has been named the NADAR (NAD and ADP-ribose) superfamily.
Pssm-ID: 271319 Cd Length: 148 Bit Score: 198.99 E-value: 8.96e-61
RibD C-terminal domain; The function of this domain is not known, but it is thought to be ...
214-418
3.08e-41
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: 148.30 E-value: 3.08e-41
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD ...
69-176
2.50e-27
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Pssm-ID: 238611 [Multi-domain] Cd Length: 115 Bit Score: 106.55 E-value: 2.50e-27
riboflavin biosynthesis protein RibD; This model describes the ribD protein as found in ...
69-418
5.27e-86
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: 272.09 E-value: 5.27e-86
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that ...
454-608
1.67e-68
conserved hypothetical protein, ribA/ribD-fused; This model describes a sequence region that occurs in at least three different polypeptide contexts. It is found fused to GTP cyclohydrolase II, the RibA of riboflavin biosynthesis (TIGR00505), as in Vibrio vulnificus. It is found fused to riboflavin biosynthesis protein RibD (TIGR00326) in rice and Arabidopsis. It occurs as a standalone protein in a number of bacterial species in varied contexts, including single gene operons and bacteriophage genomes. The member from E. coli currently is named YbiA. The function(s) of members of this family is unknown.
Pssm-ID: 274144 Cd Length: 153 Bit Score: 219.56 E-value: 1.67e-68
Pyrimidine reductase, riboflavin biosynthesis [Coenzyme transport and metabolism]; Pyrimidine ...
214-418
3.88e-66
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: 215.41 E-value: 3.88e-66
Escherichia coli swarming motility protein YbiA and related proteins; This family of ...
452-606
8.96e-61
Escherichia coli swarming motility protein YbiA and related proteins; This family of uncharacterized domains was initially classified as Domain of Unknown Function (DUF1768). It contains members such as the E. coli swarming motility protein YbiA. Mutations in YbiA cause defects in Escherichia coli swarming, but not necessarily in motility. More recently, this family has been predicted to be involved in NAD-utilizing pathways, likely to act on ADP-ribose derivatives, and has been named the NADAR (NAD and ADP-ribose) superfamily.
Pssm-ID: 271319 Cd Length: 148 Bit Score: 198.99 E-value: 8.96e-61
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: 196.45 E-value: 7.56e-59
Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain [Coenzyme transport and ...
69-367
5.71e-56
Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain [Coenzyme transport and metabolism]; Riboflavin biosynthesis protein RibD, pyrimidine deaminase domain is part of the Pathway/BioSystem: Riboflavin/FAD biosynthesis
Pssm-ID: 439887 [Multi-domain] Cd Length: 311 Bit Score: 191.81 E-value: 5.71e-56
RibD C-terminal domain; The function of this domain is not known, but it is thought to be ...
214-418
3.08e-41
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: 148.30 E-value: 3.08e-41
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD ...
69-176
2.50e-27
Riboflavin-specific deaminase. Riboflavin biosynthesis protein RibD (Diaminohydroxyphosphoribosylaminopyrimidine deaminase) catalyzes the deamination of 2,5-diamino-6-ribosylamino-4(3H)-pyrimidinone 5'-phosphate, which is an intermediate step in the biosynthesis of riboflavin.The ribG gene of Bacillus subtilis and the ribD gene of E. coli are bifunctional and contain this deaminase domain and a reductase domain which catalyzes the subsequent reduction of the ribosyl side chain.
Pssm-ID: 238611 [Multi-domain] Cd Length: 115 Bit Score: 106.55 E-value: 2.50e-27
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn ...
77-174
1.01e-04
Nucleoside deaminases include adenosine, guanine and cytosine deaminases. These enzymes are Zn dependent and catalyze the deamination of nucleosides. The zinc ion in the active site plays a central role in the proposed catalytic mechanism, activating a water molecule to form a hydroxide ion that performs a nucleophilic attack on the substrate. The functional enzyme is a homodimer. Cytosine deaminase catalyzes the deamination of cytosine to uracil and ammonia and is a member of the pyrimidine salvage pathway. Cytosine deaminase is found in bacteria and fungi but is not present in mammals; for this reason, the enzyme is currently of interest for antimicrobial drug design and gene therapy applications against tumors. Some members of this family are tRNA-specific adenosine deaminases that generate inosine at the first position of their anticodon (position 34) of specific tRNAs; this modification is thought to enlarge the codon recognition capacity during protein synthesis. Other members of the family are guanine deaminases which deaminate guanine to xanthine as part of the utilization of guanine as a nitrogen source.
Pssm-ID: 238612 [Multi-domain] Cd Length: 109 Bit Score: 41.83 E-value: 1.01e-04
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA ...
77-175
5.21e-03
tRNA(Arg) A34 adenosine deaminase TadA [Translation, ribosomal structure and biogenesis]; tRNA(Arg) A34 adenosine deaminase TadA is part of the Pathway/BioSystem: Pyrimidine salvagetRNA modification
Pssm-ID: 440355 [Multi-domain] Cd Length: 148 Bit Score: 37.79 E-value: 5.21e-03
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.
of the residues that compose this conserved feature have been mapped to the query sequence.
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