TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate ...
7-312
1.14e-116
TIM-like beta/alpha barrel domains; A large family of domains similar to triose phosphate isomerase (TIM) which, in general, share an eight beta/alpha closed barrel structure.
The actual alignment was detected with superfamily member cd02811:
Pssm-ID: 473867 [Multi-domain] Cd Length: 326 Bit Score: 340.24 E-value: 1.14e-116
Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. ...
7-312
1.14e-116
Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway.
Pssm-ID: 239205 [Multi-domain] Cd Length: 326 Bit Score: 340.24 E-value: 1.14e-116
isopentenyl-diphosphate delta-isomerase, type 2; Isopentenyl-diphosphate delta-isomerase (IPP ...
7-312
5.48e-99
isopentenyl-diphosphate delta-isomerase, type 2; Isopentenyl-diphosphate delta-isomerase (IPP isomerase) interconverts isopentenyl diphosphate and dimethylallyl diphosphate. This model represents the type 2 enzyme. FMN, NADPH, and Mg2+ are required by this form, which lacks homology to the type 1 enzyme (TIGR02150). IPP is precursor to many compounds, including enzyme cofactors, sterols, and isoprenoids. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 273999 Cd Length: 333 Bit Score: 295.71 E-value: 5.48e-99
FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl ...
21-304
3.37e-34
FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl diphosphate isomerase [Energy production and conversion, Lipid transport and metabolism, General function prediction only]; FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl diphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis
Pssm-ID: 440915 [Multi-domain] Cd Length: 357 Bit Score: 128.71 E-value: 3.37e-34
Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. ...
7-312
1.14e-116
Isopentenyl-diphosphate:dimethylallyl diphosphate isomerase type 2 (IDI-2) FMN-binding domain. Two types of IDIs have been characterized at present. The long known IDI-1 is only dependent on divalent metals for activity, whereas IDI-2 requires a metal, FMN and NADPH. IDI-2 catalyzes the interconversion of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP) in the mevalonate pathway.
Pssm-ID: 239205 [Multi-domain] Cd Length: 326 Bit Score: 340.24 E-value: 1.14e-116
isopentenyl-diphosphate delta-isomerase, type 2; Isopentenyl-diphosphate delta-isomerase (IPP ...
7-312
5.48e-99
isopentenyl-diphosphate delta-isomerase, type 2; Isopentenyl-diphosphate delta-isomerase (IPP isomerase) interconverts isopentenyl diphosphate and dimethylallyl diphosphate. This model represents the type 2 enzyme. FMN, NADPH, and Mg2+ are required by this form, which lacks homology to the type 1 enzyme (TIGR02150). IPP is precursor to many compounds, including enzyme cofactors, sterols, and isoprenoids. [Biosynthesis of cofactors, prosthetic groups, and carriers, Other]
Pssm-ID: 273999 Cd Length: 333 Bit Score: 295.71 E-value: 5.48e-99
FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl ...
21-304
3.37e-34
FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl diphosphate isomerase [Energy production and conversion, Lipid transport and metabolism, General function prediction only]; FMN-dependent dehydrogenase, includes L-lactate dehydrogenase and type II isopentenyl diphosphate isomerase is part of the Pathway/BioSystem: Isoprenoid biosynthesis
Pssm-ID: 440915 [Multi-domain] Cd Length: 357 Bit Score: 128.71 E-value: 3.37e-34
TIM barrel proteins share a structurally conserved phosphate binding motif and in general ...
60-278
3.59e-05
TIM barrel proteins share a structurally conserved phosphate binding motif and in general share an eight beta/alpha closed barrel structure. Specific for this family is the conserved phosphate binding site at the edges of strands 7 and 8. The phosphate comes either from the substrate, as in the case of inosine monophosphate dehydrogenase (IMPDH), or from ribulose-5-phosphate 3-epimerase (RPE) or from cofactors, like FMN.
Pssm-ID: 240073 [Multi-domain] Cd Length: 200 Bit Score: 44.11 E-value: 3.59e-05
Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in ...
251-304
6.19e-05
Family of homologous FMN-dependent alpha-hydroxyacid oxidizing enzymes. This family occurs in both prokaryotes and eukaryotes. Members of this family include flavocytochrome b2 (FCB2), glycolate oxidase (GOX), lactate monooxygenase (LMO), mandelate dehydrogenase (MDH), and long chain hydroxyacid oxidase (LCHAO). In green plants, glycolate oxidase is one of the key enzymes in photorespiration where it oxidizes glycolate to glyoxylate. LMO catalyzes the oxidation of L-lactate to acetate and carbon dioxide. MDH oxidizes (S)-mandelate to phenylglyoxalate. It is an enzyme in the mandelate pathway that occurs in several strains of Pseudomonas which converts (R)-mandelate to benzoate.
Pssm-ID: 239203 [Multi-domain] Cd Length: 299 Bit Score: 43.98 E-value: 6.19e-05
Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that ...
252-282
3.53e-04
Glutamate synthase (GltS) FMN-binding domain. GltS is a complex iron-sulfur flavoprotein that catalyzes the reductive synthesis of L-glutamate from 2-oxoglutarate and L-glutamine via intramolecular channelling of ammonia, a reaction in the plant, yeast and bacterial pathway for ammonia assimilation. It is a multifunctional enzyme that functions through three distinct active centers, carrying out L-glutamine hydrolysis, conversion of 2-oxoglutarate into L-glutamate, and electron uptake from an electron donor.
Pssm-ID: 239202 [Multi-domain] Cd Length: 392 Bit Score: 42.14 E-value: 3.53e-04
Flavocytochrome b2 (FCB2) FMN-binding domain. FCB2 (AKA L-lactate:cytochrome c oxidoreductase) is a respiratory enzyme located in the intermembrane space of fungal mitochondria which catalyzes the oxidation of L-lactate to pyruvate. FCB2 also participates in a short electron-transport chain involving cytochrome c and cytochrome oxidase which ultimately directs the reducing equivalents gained from L-lactate oxidation to oxygen, yielding one molecule of ATP for every L-lactate molecule consumed. FCB2 is composed of 2 domains: a C-terminal flavin-binding domain, which includes the active site for lacate oxidation, and an N-terminal b2-cytochrome domain, required for efficient cytochrome c reduction. FCB2 is a homotetramer and contains two noncovalently bound cofactors, FMN and heme per subunit.
Pssm-ID: 239238 [Multi-domain] Cd Length: 344 Bit Score: 40.27 E-value: 1.13e-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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