CofD/YvcK family protein similar to Bacillus subtilis gluconeogenesis factor YvcK, which is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway and may play a role in carbon metabolism, and related to CofD, a 2-phospho-L-lactate transferase involved in F420 biosynthesis
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate ...
12-299
9.42e-133
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but have different substrate binding residues conserved within each family.
The actual alignment was detected with superfamily member TIGR01826:
Pssm-ID: 444899 Cd Length: 310 Bit Score: 378.96 E-value: 9.42e-133
conserved hypothetical protein, cofD-related; This model represents a subfamily of conserved ...
12-299
9.42e-133
conserved hypothetical protein, cofD-related; This model represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (TIGR01819), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis. Both this family and TIGR01819 are within the scope of the pfam01933. [Hypothetical proteins, Conserved]
Pssm-ID: 211689 Cd Length: 310 Bit Score: 378.96 E-value: 9.42e-133
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family ...
4-296
1.89e-117
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family [Carbohydrate transport and metabolism, Coenzyme transport and metabolism];
Pssm-ID: 440160 Cd Length: 314 Bit Score: 340.19 E-value: 1.89e-117
family of mostly uncharacterized proteins similar to B.subtilis YvcK; One member of this ...
12-296
3.86e-96
family of mostly uncharacterized proteins similar to B.subtilis YvcK; One member of this protein family, YvcK from Bacillus subtilis, has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway. In general, this family of mostly uncharacterized proteins is related to the CofD-like protein family. CofD has been characterized as a 2-phospho-L-lactate transferase involved in F420 biosynthesis. This family appears to have the same conserved phosphate binding site as the other family in this hierarchy, but a different substrate binding site.
Pssm-ID: 132873 Cd Length: 308 Bit Score: 286.00 E-value: 3.86e-96
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase ...
12-257
4.84e-96
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyzes the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices.
Pssm-ID: 426519 Cd Length: 249 Bit Score: 283.56 E-value: 4.84e-96
conserved hypothetical protein, cofD-related; This model represents a subfamily of conserved ...
12-299
9.42e-133
conserved hypothetical protein, cofD-related; This model represents a subfamily of conserved hypothetical proteins that forms a sister group to the family of CofD, (TIGR01819), LPPG:Fo 2-phospho-L-lactate transferase, an enzyme of cytochrome F420 biosynthesis. Both this family and TIGR01819 are within the scope of the pfam01933. [Hypothetical proteins, Conserved]
Pssm-ID: 211689 Cd Length: 310 Bit Score: 378.96 E-value: 9.42e-133
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family ...
4-296
1.89e-117
Archaeal 2-phospho-L-lactate transferase/Bacterial gluconeogenesis factor, CofD/UPF0052 family [Carbohydrate transport and metabolism, Coenzyme transport and metabolism];
Pssm-ID: 440160 Cd Length: 314 Bit Score: 340.19 E-value: 1.89e-117
family of mostly uncharacterized proteins similar to B.subtilis YvcK; One member of this ...
12-296
3.86e-96
family of mostly uncharacterized proteins similar to B.subtilis YvcK; One member of this protein family, YvcK from Bacillus subtilis, has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and the pentose phosphate pathway. In general, this family of mostly uncharacterized proteins is related to the CofD-like protein family. CofD has been characterized as a 2-phospho-L-lactate transferase involved in F420 biosynthesis. This family appears to have the same conserved phosphate binding site as the other family in this hierarchy, but a different substrate binding site.
Pssm-ID: 132873 Cd Length: 308 Bit Score: 286.00 E-value: 3.86e-96
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase ...
12-257
4.84e-96
2-phospho-L-lactate transferase CofD; This entry contains 2-phospho-L-lactate transferase (CofD), phosphoenolpyruvate transferase and related sequences. CofD catalyzes the fourth step in the biosynthesis of coenzyme F420, which is the transfer of the 2-phospholactate moiety from lactyl (2)diphospho-(5') guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin (FO) with the formation of the L-lactyl phosphodiester of 7,8-didemethyl- 8-hydroxy-5-deazariboflavin (F420-0) and GMP. F420 is a flavin derivative found in methanogens, Mycobacteria, and several other lineages. This enzyme is characterized so far in Methanocaldococcus jannaschii (Methanococcus jannaschii) but appears restricted to F420-containing species and is predicted to carry out the same function in these other species. CofD monomer contains 12 beta- strands, seven of them form a Rossmann fold, and 13 alpha-helices.
Pssm-ID: 426519 Cd Length: 249 Bit Score: 283.56 E-value: 4.84e-96
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate ...
12-257
2.46e-41
Family of CofD-like proteins and proteins related to YvcK; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis. YvcK from Bacillus subtilis is a member of a family of mostly uncharacterized proteins and has been proposed to play a role in carbon metabolism, since its function is essential for growth on intermediates of the Krebs cycle and pentose phosphate pathway. Both families appear to have a conserved phosphate binding site, but have different substrate binding residues conserved within each family.
Pssm-ID: 132871 Cd Length: 309 Bit Score: 145.42 E-value: 2.46e-41
LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; CofD is a ...
82-234
1.19e-11
LPPG:FO 2-phospho-L-lactate transferase; important in F420 biosynthesis; CofD is a 2-phospho-L-lactate transferase that catalyzes the last step in the biosynthesis of coenzyme F(420)-0 (F(420) without polyglutamate) by transferring the lactyl phosphate moiety of lactyl(2)diphospho-(5')guanosine (LPPG) to 7,8-didemethyl-8-hydroxy-5-deazariboflavin ribitol (F0). F420 is a hydride carrier, important for energy metabolism of methanogenic archaea, as well as for the biosynthesis of other natural products, like tetracycline in Streptomyces. F420 and some of its precursors are also utilized as cofactors for enzymes, like DNA photolyase in Mycobacterium tuberculosis.
Pssm-ID: 132872 Cd Length: 303 Bit Score: 64.16 E-value: 1.19e-11
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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