6-phosphogluconate dehydrogenase, decarboxylating [Candidatus Saccharibacteria bacterium RAAC3_TM7_1]
Protein Classification
List of domain hits
| Name | Accession | Description | Interval | E-value | |||||
| YqeC super family | cl34065 | 6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]; |
1-296 | 4.59e-142 | |||||
6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]; The actual alignment was detected with superfamily member COG1023: Pssm-ID: 440646 [Multi-domain] Cd Length: 300 Bit Score: 402.16 E-value: 4.59e-142
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| Name | Accession | Description | Interval | E-value | |||||
| YqeC | COG1023 | 6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]; |
1-296 | 4.59e-142 | |||||
6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]; Pssm-ID: 440646 [Multi-domain] Cd Length: 300 Bit Score: 402.16 E-value: 4.59e-142
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| PRK09599 | PRK09599 | NADP-dependent phosphogluconate dehydrogenase; |
1-296 | 6.02e-124 | |||||
NADP-dependent phosphogluconate dehydrogenase; Pssm-ID: 236582 [Multi-domain] Cd Length: 301 Bit Score: 356.37 E-value: 6.02e-124
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| gnd_rel | TIGR00872 | 6-phosphogluconate dehydrogenase (decarboxylating); This family resembles a larger family (gnd) ... |
1-296 | 1.06e-89 | |||||
6-phosphogluconate dehydrogenase (decarboxylating); This family resembles a larger family (gnd) of bacterial and eukaryotic 6-phosphogluconate dehydrogenases but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain gnd, and in Aquifex aeolicus. The protein from Methylobacillus flagellatus KT has been characterized as a decarboxylating 6-phosphogluconate dehydrogenase as part of an unusual formaldehyde oxidation cycle. In some sequenced organisms members of this family are the sole 6-phosphogluconate dehydrogenase present and are probably active in the pentose phosphate cycle. [Energy metabolism, Pentose phosphate pathway] Pssm-ID: 273313 [Multi-domain] Cd Length: 298 Bit Score: 269.41 E-value: 1.06e-89
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| NAD_binding_2 | pfam03446 | NAD binding domain of 6-phosphogluconate dehydrogenase; The NAD binding domain of ... |
2-153 | 1.97e-32 | |||||
NAD binding domain of 6-phosphogluconate dehydrogenase; The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold. Pssm-ID: 427298 [Multi-domain] Cd Length: 159 Bit Score: 117.57 E-value: 1.97e-32
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| SDR_a4 | cd05266 | atypical (a) SDRs, subgroup 4; Atypical SDRs in this subgroup are poorly defined, one member ... |
3-90 | 6.17e-06 | |||||
atypical (a) SDRs, subgroup 4; Atypical SDRs in this subgroup are poorly defined, one member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is related to, but is different from, the archetypical SDRs, GXGXXG. This subgroup also lacks most of the characteristic active site residues of the SDRs; however, the upstream Ser is present at the usual place, and some potential catalytic residues are present in place of the usual YXXXK active site motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Pssm-ID: 187576 [Multi-domain] Cd Length: 251 Bit Score: 46.54 E-value: 6.17e-06
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| Name | Accession | Description | Interval | E-value | |||||
| YqeC | COG1023 | 6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]; |
1-296 | 4.59e-142 | |||||
6-phosphogluconate dehydrogenase (decarboxylating) [Carbohydrate transport and metabolism]; Pssm-ID: 440646 [Multi-domain] Cd Length: 300 Bit Score: 402.16 E-value: 4.59e-142
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| PRK09599 | PRK09599 | NADP-dependent phosphogluconate dehydrogenase; |
1-296 | 6.02e-124 | |||||
NADP-dependent phosphogluconate dehydrogenase; Pssm-ID: 236582 [Multi-domain] Cd Length: 301 Bit Score: 356.37 E-value: 6.02e-124
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| gnd_rel | TIGR00872 | 6-phosphogluconate dehydrogenase (decarboxylating); This family resembles a larger family (gnd) ... |
1-296 | 1.06e-89 | |||||
6-phosphogluconate dehydrogenase (decarboxylating); This family resembles a larger family (gnd) of bacterial and eukaryotic 6-phosphogluconate dehydrogenases but differs from it by a deep split in a UPGMA similarity clustering tree and the lack of a central region of about 140 residues. Among complete genomes, it is found is found in Bacillus subtilis and Mycobacterium tuberculosis, both of which also contain gnd, and in Aquifex aeolicus. The protein from Methylobacillus flagellatus KT has been characterized as a decarboxylating 6-phosphogluconate dehydrogenase as part of an unusual formaldehyde oxidation cycle. In some sequenced organisms members of this family are the sole 6-phosphogluconate dehydrogenase present and are probably active in the pentose phosphate cycle. [Energy metabolism, Pentose phosphate pathway] Pssm-ID: 273313 [Multi-domain] Cd Length: 298 Bit Score: 269.41 E-value: 1.06e-89
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| gnd | TIGR00873 | 6-phosphogluconate dehydrogenase (decarboxylating); This model does not specify whether the ... |
3-287 | 7.14e-47 | |||||
6-phosphogluconate dehydrogenase (decarboxylating); This model does not specify whether the cofactor is NADP only (EC 1.1.1.44), NAD only, or both. The model does not assign an EC number for that reason. [Energy metabolism, Pentose phosphate pathway] Pssm-ID: 273314 [Multi-domain] Cd Length: 467 Bit Score: 163.73 E-value: 7.14e-47
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| PTZ00142 | PTZ00142 | 6-phosphogluconate dehydrogenase; Provisional |
3-287 | 2.32e-42 | |||||
6-phosphogluconate dehydrogenase; Provisional Pssm-ID: 240287 [Multi-domain] Cd Length: 470 Bit Score: 151.48 E-value: 2.32e-42
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| Gnd | COG0362 | 6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; 6-phosphogluconate ... |
3-274 | 9.98e-42 | |||||
6-phosphogluconate dehydrogenase [Carbohydrate transport and metabolism]; 6-phosphogluconate dehydrogenase is part of the Pathway/BioSystem: Pentose phosphate pathway Pssm-ID: 440131 [Multi-domain] Cd Length: 467 Bit Score: 149.84 E-value: 9.98e-42
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| PRK09287 | PRK09287 | NADP-dependent phosphogluconate dehydrogenase; |
11-287 | 1.85e-37 | |||||
NADP-dependent phosphogluconate dehydrogenase; Pssm-ID: 236453 [Multi-domain] Cd Length: 459 Bit Score: 138.33 E-value: 1.85e-37
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| MmsB | COG2084 | 3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport ... |
1-194 | 8.29e-33 | |||||
3-hydroxyisobutyrate dehydrogenase or related beta-hydroxyacid dehydrogenase [Lipid transport and metabolism]; Pssm-ID: 441687 [Multi-domain] Cd Length: 285 Bit Score: 122.15 E-value: 8.29e-33
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| PLN02350 | PLN02350 | phosphogluconate dehydrogenase (decarboxylating) |
2-274 | 1.74e-32 | |||||
phosphogluconate dehydrogenase (decarboxylating) Pssm-ID: 215200 [Multi-domain] Cd Length: 493 Bit Score: 125.21 E-value: 1.74e-32
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| NAD_binding_2 | pfam03446 | NAD binding domain of 6-phosphogluconate dehydrogenase; The NAD binding domain of ... |
2-153 | 1.97e-32 | |||||
NAD binding domain of 6-phosphogluconate dehydrogenase; The NAD binding domain of 6-phosphogluconate dehydrogenase adopts a Rossmann fold. Pssm-ID: 427298 [Multi-domain] Cd Length: 159 Bit Score: 117.57 E-value: 1.97e-32
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| 6PGD | pfam00393 | 6-phosphogluconate dehydrogenase, C-terminal domain; This family represents the C-terminal ... |
168-274 | 5.53e-16 | |||||
6-phosphogluconate dehydrogenase, C-terminal domain; This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each. Pssm-ID: 459797 Cd Length: 290 Bit Score: 76.34 E-value: 5.53e-16
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| garR | PRK11559 | tartronate semialdehyde reductase; Provisional |
1-154 | 1.84e-14 | |||||
tartronate semialdehyde reductase; Provisional Pssm-ID: 183197 [Multi-domain] Cd Length: 296 Bit Score: 72.01 E-value: 1.84e-14
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| PRK15059 | PRK15059 | 2-hydroxy-3-oxopropionate reductase; |
1-189 | 1.44e-09 | |||||
2-hydroxy-3-oxopropionate reductase; Pssm-ID: 185019 [Multi-domain] Cd Length: 292 Bit Score: 57.72 E-value: 1.44e-09
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| TyrA | COG0287 | Prephenate dehydrogenase [Amino acid transport and metabolism]; Prephenate dehydrogenase is ... |
1-94 | 2.57e-09 | |||||
Prephenate dehydrogenase [Amino acid transport and metabolism]; Prephenate dehydrogenase is part of the Pathway/BioSystem: Aromatic amino acid biosynthesis Pssm-ID: 440056 [Multi-domain] Cd Length: 278 Bit Score: 57.06 E-value: 2.57e-09
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| 2-Hacid_dh_C | pfam02826 | D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted ... |
1-47 | 1.47e-07 | |||||
D-isomer specific 2-hydroxyacid dehydrogenase, NAD binding domain; This domain is inserted into the catalytic domain, the large dehydrogenase and D-lactate dehydrogenase families in SCOP. N-terminal portion of which is represented by family pfam00389. Pssm-ID: 427007 [Multi-domain] Cd Length: 178 Bit Score: 50.57 E-value: 1.47e-07
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| COG5495 | COG5495 | Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains ... |
1-91 | 1.81e-07 | |||||
Predicted oxidoreductase, contains short-chain dehydrogenase (SDR) and DUF2520 domains [General function prediction only]; Pssm-ID: 444246 [Multi-domain] Cd Length: 286 Bit Score: 51.35 E-value: 1.81e-07
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| TrkA | COG0569 | Trk/Ktr K+ transport system regulatory component TrkA/KtrA/KtrC, RCK domain [Inorganic ion ... |
1-64 | 4.77e-07 | |||||
Trk/Ktr K+ transport system regulatory component TrkA/KtrA/KtrC, RCK domain [Inorganic ion transport and metabolism, Signal transduction mechanisms]; Pssm-ID: 440335 [Multi-domain] Cd Length: 296 Bit Score: 50.45 E-value: 4.77e-07
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| PRK15461 | PRK15461 | sulfolactaldehyde 3-reductase; |
2-270 | 6.79e-07 | |||||
sulfolactaldehyde 3-reductase; Pssm-ID: 185358 [Multi-domain] Cd Length: 296 Bit Score: 49.85 E-value: 6.79e-07
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| PRK07417 | PRK07417 | prephenate/arogenate dehydrogenase; |
1-94 | 7.44e-07 | |||||
prephenate/arogenate dehydrogenase; Pssm-ID: 180970 [Multi-domain] Cd Length: 279 Bit Score: 49.51 E-value: 7.44e-07
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| FadB | COG1250 | 3-hydroxyacyl-CoA dehydrogenase [Lipid transport and metabolism]; 3-hydroxyacyl-CoA ... |
1-51 | 1.49e-06 | |||||
3-hydroxyacyl-CoA dehydrogenase [Lipid transport and metabolism]; 3-hydroxyacyl-CoA dehydrogenase is part of the Pathway/BioSystem: Fatty acid biosynthesis Pssm-ID: 440862 [Multi-domain] Cd Length: 281 Bit Score: 48.57 E-value: 1.49e-06
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| COG2085 | COG2085 | Predicted dinucleotide-binding enzyme [General function prediction only]; |
3-95 | 1.86e-06 | |||||
Predicted dinucleotide-binding enzyme [General function prediction only]; Pssm-ID: 441688 [Multi-domain] Cd Length: 205 Bit Score: 47.47 E-value: 1.86e-06
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| SDR_a4 | cd05266 | atypical (a) SDRs, subgroup 4; Atypical SDRs in this subgroup are poorly defined, one member ... |
3-90 | 6.17e-06 | |||||
atypical (a) SDRs, subgroup 4; Atypical SDRs in this subgroup are poorly defined, one member is identified as a putative NAD-dependent epimerase/dehydratase. Atypical SDRs are distinct from classical SDRs. Members of this subgroup have a glycine-rich NAD(P)-binding motif that is related to, but is different from, the archetypical SDRs, GXGXXG. This subgroup also lacks most of the characteristic active site residues of the SDRs; however, the upstream Ser is present at the usual place, and some potential catalytic residues are present in place of the usual YXXXK active site motif. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Pssm-ID: 187576 [Multi-domain] Cd Length: 251 Bit Score: 46.54 E-value: 6.17e-06
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| 3HCDH_N | pfam02737 | 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda ... |
2-42 | 1.10e-05 | |||||
3-hydroxyacyl-CoA dehydrogenase, NAD binding domain; This family also includes lambda crystallin. Pssm-ID: 397037 [Multi-domain] Cd Length: 180 Bit Score: 45.22 E-value: 1.10e-05
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| trkA | PRK09496 | Trk system potassium transporter TrkA; |
1-64 | 1.27e-05 | |||||
Trk system potassium transporter TrkA; Pssm-ID: 236541 [Multi-domain] Cd Length: 453 Bit Score: 46.27 E-value: 1.27e-05
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| formate_dh_like | cd05198 | Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase ... |
1-39 | 3.52e-05 | |||||
Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxy acid dehydrogenase family; Formate dehydrogenase, D-specific 2-hydroxy acid dehydrogenase, Phosphoglycerate Dehydrogenase, Lactate dehydrogenase, Thermostable Phosphite Dehydrogenase, and Hydroxy(phenyl)pyruvate reductase, among others, share a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. 2-hydroxyacid dehydrogenases are enzymes that catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase, among others. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240622 [Multi-domain] Cd Length: 302 Bit Score: 44.54 E-value: 3.52e-05
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| Mand_dh_like | cd12168 | D-Mandelate Dehydrogenase-like dehydrogenases; D-Mandelate dehydrogenase (D-ManDH), identified ... |
1-48 | 1.13e-04 | |||||
D-Mandelate Dehydrogenase-like dehydrogenases; D-Mandelate dehydrogenase (D-ManDH), identified as an enzyme that interconverts benzoylformate and D-mandelate, is a D-2-hydroxyacid dehydrogenase family member that catalyzes the conversion of c3-branched 2-ketoacids. D-ManDH exhibits broad substrate specificities for 2-ketoacids with large hydrophobic side chains, particularly those with C3-branched side chains. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Glycerate dehydrogenase catalyzes the reaction (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240645 [Multi-domain] Cd Length: 321 Bit Score: 42.92 E-value: 1.13e-04
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| ProC | COG0345 | Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; ... |
1-56 | 1.17e-04 | |||||
Pyrroline-5-carboxylate reductase [Amino acid transport and metabolism]; Pyrroline-5-carboxylate reductase is part of the Pathway/BioSystem: Proline biosynthesis Pssm-ID: 440114 [Multi-domain] Cd Length: 267 Bit Score: 42.74 E-value: 1.17e-04
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| 2-Hacid_dh_1 | cd05300 | Putative D-isomer specific 2-hydroxyacid dehydrogenase; 2-Hydroxyacid dehydrogenases catalyze ... |
2-40 | 1.57e-04 | |||||
Putative D-isomer specific 2-hydroxyacid dehydrogenase; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomains but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Formate dehydrogenase (FDH) catalyzes the NAD+-dependent oxidation of formate ion to carbon dioxide with the concomitant reduction of NAD+ to NADH. FDHs of this family contain no metal ions or prosthetic groups. Catalysis occurs though direct transfer of the hydride ion to NAD+ without the stages of acid-base catalysis typically found in related dehydrogenases. FDHs are found in all methylotrophic microorganisms in energy production and in the stress responses of plants. Pssm-ID: 240625 [Multi-domain] Cd Length: 313 Bit Score: 42.51 E-value: 1.57e-04
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| F420_oxidored | pfam03807 | NADP oxidoreductase coenzyme F420-dependent; |
4-92 | 1.60e-04 | |||||
NADP oxidoreductase coenzyme F420-dependent; Pssm-ID: 397743 [Multi-domain] Cd Length: 92 Bit Score: 39.91 E-value: 1.60e-04
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| 2-Hacid_dh_13 | cd12178 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
3-45 | 1.82e-04 | |||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240655 [Multi-domain] Cd Length: 317 Bit Score: 42.61 E-value: 1.82e-04
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| PLN02256 | PLN02256 | arogenate dehydrogenase |
1-33 | 1.91e-04 | |||||
arogenate dehydrogenase Pssm-ID: 215144 [Multi-domain] Cd Length: 304 Bit Score: 42.34 E-value: 1.91e-04
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| YbjT | COG0702 | Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General ... |
2-57 | 1.99e-04 | |||||
Uncharacterized conserved protein YbjT, contains NAD(P)-binding and DUF2867 domains [General function prediction only]; Pssm-ID: 440466 [Multi-domain] Cd Length: 215 Bit Score: 41.75 E-value: 1.99e-04
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| YwnB | COG2910 | Putative NADH-flavin reductase [General function prediction only]; |
2-59 | 2.09e-04 | |||||
Putative NADH-flavin reductase [General function prediction only]; Pssm-ID: 442154 [Multi-domain] Cd Length: 205 Bit Score: 41.77 E-value: 2.09e-04
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| 2-Hacid_dh_6 | cd12165 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
1-39 | 2.85e-04 | |||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240642 [Multi-domain] Cd Length: 314 Bit Score: 41.85 E-value: 2.85e-04
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| TrkA_N | pfam02254 | TrkA-N domain; This domain is found in a wide variety of proteins. These proteins include ... |
3-48 | 3.12e-04 | |||||
TrkA-N domain; This domain is found in a wide variety of proteins. These proteins include potassium channels, phosphoesterases, and various other transporters. This domain binds to NAD. Pssm-ID: 426679 [Multi-domain] Cd Length: 115 Bit Score: 39.43 E-value: 3.12e-04
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| GDH_like_2 | cd12164 | Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy ... |
1-37 | 5.39e-04 | |||||
Putative glycerate dehydrogenase and related proteins of the D-specific 2-hydroxy dehydrogenase family; This group contains a variety of proteins variously identified as glycerate dehydrogenase (GDH, also known as hydroxypyruvate reductase) and other enzymes of the 2-hydroxyacid dehydrogenase family. GDH catalyzes the reversible reaction of (R)-glycerate + NAD+ to hydroxypyruvate + NADH + H+. 2-hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann-fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240641 [Multi-domain] Cd Length: 306 Bit Score: 40.94 E-value: 5.39e-04
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| PLN02858 | PLN02858 | fructose-bisphosphate aldolase |
2-175 | 5.95e-04 | |||||
fructose-bisphosphate aldolase Pssm-ID: 215463 [Multi-domain] Cd Length: 1378 Bit Score: 41.38 E-value: 5.95e-04
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| PRK14806 | PRK14806 | bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; ... |
2-94 | 6.09e-04 | |||||
bifunctional cyclohexadienyl dehydrogenase/ 3-phosphoshikimate 1-carboxyvinyltransferase; Provisional Pssm-ID: 237820 [Multi-domain] Cd Length: 735 Bit Score: 41.13 E-value: 6.09e-04
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| PRK07530 | PRK07530 | 3-hydroxybutyryl-CoA dehydrogenase; Validated |
2-41 | 6.81e-04 | |||||
3-hydroxybutyryl-CoA dehydrogenase; Validated Pssm-ID: 181018 [Multi-domain] Cd Length: 292 Bit Score: 40.76 E-value: 6.81e-04
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| PRK06522 | PRK06522 | 2-dehydropantoate 2-reductase; Reviewed |
1-45 | 8.20e-04 | |||||
2-dehydropantoate 2-reductase; Reviewed Pssm-ID: 235821 [Multi-domain] Cd Length: 304 Bit Score: 40.22 E-value: 8.20e-04
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| PGDH_like_1 | cd12169 | Putative D-3-Phosphoglycerate Dehydrogenases; Phosphoglycerate dehydrogenases (PGDHs) catalyze ... |
2-51 | 9.43e-04 | |||||
Putative D-3-Phosphoglycerate Dehydrogenases; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. Pssm-ID: 240646 [Multi-domain] Cd Length: 308 Bit Score: 40.19 E-value: 9.43e-04
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| 2-Hacid_dh_11 | cd12175 | Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; ... |
2-47 | 9.44e-04 | |||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases, NAD-binding and catalytic domains; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240652 [Multi-domain] Cd Length: 311 Bit Score: 40.25 E-value: 9.44e-04
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| GpsA | COG0240 | Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Glycerol-3-phosphate ... |
1-91 | 1.00e-03 | |||||
Glycerol-3-phosphate dehydrogenase [Energy production and conversion]; Glycerol-3-phosphate dehydrogenase is part of the Pathway/BioSystem: Isoprenoid biosynthesis Pssm-ID: 440010 [Multi-domain] Cd Length: 327 Bit Score: 40.02 E-value: 1.00e-03
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| BVR-B_like_SDR_a | cd05244 | biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; ... |
2-59 | 1.12e-03 | |||||
biliverdin IX beta reductase (BVR-B, aka flavin reductase)-like proteins; atypical (a) SDRs; Human BVR-B catalyzes pyridine nucleotide-dependent production of bilirubin-IX beta during fetal development; in the adult BVR-B has flavin and ferric reductase activities. Human BVR-B catalyzes the reduction of FMN, FAD, and riboflavin. Recognition of flavin occurs mostly by hydrophobic interactions, accounting for the broad substrate specificity. Atypical SDRs are distinct from classical SDRs. BVR-B does not share the key catalytic triad, or conserved tyrosine typical of SDRs. The glycine-rich NADP-binding motif of BVR-B is GXXGXXG, which is similar but not identical to the pattern seen in extended SDRs. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Atypical SDRs include biliverdin IX beta reductase (BVR-B,aka flavin reductase), NMRa (a negative transcriptional regulator of various fungi), progesterone 5-beta-reductase like proteins, phenylcoumaran benzylic ether and pinoresinol-lariciresinol reductases, phenylpropene synthases, eugenol synthase, triphenylmethane reductase, isoflavone reductases, and others. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. In addition to the Rossmann fold core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids, and typically have a TGXXGXXG cofactor binding motif. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif. Pssm-ID: 187555 [Multi-domain] Cd Length: 207 Bit Score: 39.53 E-value: 1.12e-03
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| LdhA | COG1052 | Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase [Energy production and conversion, ... |
1-45 | 1.22e-03 | |||||
Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase [Energy production and conversion, Coenzyme transport and metabolism, General function prediction only]; Lactate dehydrogenase or related 2-hydroxyacid dehydrogenase is part of the Pathway/BioSystem: Pyridoxal phosphate biosynthesis Pssm-ID: 440672 [Multi-domain] Cd Length: 316 Bit Score: 39.69 E-value: 1.22e-03
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| PRK08268 | PRK08268 | 3-hydroxy-acyl-CoA dehydrogenase; Validated |
2-42 | 1.24e-03 | |||||
3-hydroxy-acyl-CoA dehydrogenase; Validated Pssm-ID: 236211 [Multi-domain] Cd Length: 507 Bit Score: 40.22 E-value: 1.24e-03
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| CAD1 | cd05283 | Cinnamyl alcohol dehydrogenases (CAD); Cinnamyl alcohol dehydrogenases (CAD), members of the ... |
1-45 | 1.41e-03 | |||||
Cinnamyl alcohol dehydrogenases (CAD); Cinnamyl alcohol dehydrogenases (CAD), members of the medium chain dehydrogenase/reductase family, reduce cinnamaldehydes to cinnamyl alcohols in the last step of monolignal metabolism in plant cells walls. CAD binds 2 zinc ions and is NADPH- dependent. CAD family members are also found in non-plant species, e.g. in yeast where they have an aldehyde reductase activity. The medium chain dehydrogenases/reductase (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH), quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. Active site zinc has a catalytic role, while structural zinc aids in stability. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Pssm-ID: 176186 [Multi-domain] Cd Length: 337 Bit Score: 39.79 E-value: 1.41e-03
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| PGDH_like_2 | cd12172 | Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; ... |
2-45 | 2.14e-03 | |||||
Putative D-3-Phosphoglycerate Dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily, which also include groups such as L-alanine dehydrogenase and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Many, not all, members of this family are dimeric. Pssm-ID: 240649 [Multi-domain] Cd Length: 306 Bit Score: 39.01 E-value: 2.14e-03
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| PRK08293 | PRK08293 | 3-hydroxyacyl-CoA dehydrogenase; |
2-39 | 2.67e-03 | |||||
3-hydroxyacyl-CoA dehydrogenase; Pssm-ID: 181359 [Multi-domain] Cd Length: 287 Bit Score: 38.77 E-value: 2.67e-03
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| PLN02545 | PLN02545 | 3-hydroxybutyryl-CoA dehydrogenase |
2-41 | 2.86e-03 | |||||
3-hydroxybutyryl-CoA dehydrogenase Pssm-ID: 215300 [Multi-domain] Cd Length: 295 Bit Score: 38.56 E-value: 2.86e-03
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| PLN02712 | PLN02712 | arogenate dehydrogenase |
1-32 | 3.46e-03 | |||||
arogenate dehydrogenase Pssm-ID: 215382 [Multi-domain] Cd Length: 667 Bit Score: 38.81 E-value: 3.46e-03
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| 6PGD | pfam00393 | 6-phosphogluconate dehydrogenase, C-terminal domain; This family represents the C-terminal ... |
171-296 | 3.58e-03 | |||||
6-phosphogluconate dehydrogenase, C-terminal domain; This family represents the C-terminal all-alpha domain of 6-phosphogluconate dehydrogenase. The domain contains two structural repeats of 5 helices each. Pssm-ID: 459797 Cd Length: 290 Bit Score: 38.20 E-value: 3.58e-03
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| 2-Hacid_dh_2 | cd12159 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
1-39 | 4.14e-03 | |||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240636 Cd Length: 303 Bit Score: 38.40 E-value: 4.14e-03
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| PRK11880 | PRK11880 | pyrroline-5-carboxylate reductase; Reviewed |
1-56 | 4.19e-03 | |||||
pyrroline-5-carboxylate reductase; Reviewed Pssm-ID: 237008 [Multi-domain] Cd Length: 267 Bit Score: 38.20 E-value: 4.19e-03
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| 2-Hacid_dh_5 | cd12163 | Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze ... |
1-39 | 4.88e-03 | |||||
Putative D-isomer specific 2-hydroxyacid dehydrogenases; 2-Hydroxyacid dehydrogenases catalyze the conversion of a wide variety of D-2-hydroxy acids to their corresponding keto acids. The general mechanism is (R)-lactate + acceptor to pyruvate + reduced acceptor. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240640 Cd Length: 334 Bit Score: 38.02 E-value: 4.88e-03
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| PRK06130 | PRK06130 | 3-hydroxybutyryl-CoA dehydrogenase; Validated |
3-56 | 4.89e-03 | |||||
3-hydroxybutyryl-CoA dehydrogenase; Validated Pssm-ID: 235707 [Multi-domain] Cd Length: 311 Bit Score: 38.22 E-value: 4.89e-03
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| CtBP_dh | cd05299 | C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related ... |
1-47 | 5.46e-03 | |||||
C-terminal binding protein (CtBP), D-isomer-specific 2-hydroxyacid dehydrogenases related repressor; The transcriptional corepressor CtBP is a dehydrogenase with sequence and structural similarity to the d2-hydroxyacid dehydrogenase family. CtBP was initially identified as a protein that bound the PXDLS sequence at the adenovirus E1A C terminus, causing the loss of CR-1-mediated transactivation. CtBP binds NAD(H) within a deep cleft, undergoes a conformational change upon NAD binding, and has NAD-dependent dehydrogenase activity. Pssm-ID: 240624 [Multi-domain] Cd Length: 312 Bit Score: 37.88 E-value: 5.46e-03
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| MDR | cd05188 | Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; ... |
2-105 | 5.59e-03 | |||||
Medium chain reductase/dehydrogenase (MDR)/zinc-dependent alcohol dehydrogenase-like family; The medium chain reductase/dehydrogenases (MDR)/zinc-dependent alcohol dehydrogenase-like family, which contains the zinc-dependent alcohol dehydrogenase (ADH-Zn) and related proteins, is a diverse group of proteins related to the first identified member, class I mammalian ADH. MDRs display a broad range of activities and are distinguished from the smaller short chain dehydrogenases (~ 250 amino acids vs. the ~ 350 amino acids of the MDR). The MDR proteins have 2 domains: a C-terminal NAD(P) binding-Rossmann fold domain of a beta-alpha form and an N-terminal catalytic domain with distant homology to GroES. The MDR group contains a host of activities, including the founding alcohol dehydrogenase (ADH) , quinone reductase, sorbitol dehydrogenase, formaldehyde dehydrogenase, butanediol DH, ketose reductase, cinnamyl reductase, and numerous others. The zinc-dependent alcohol dehydrogenases (ADHs) catalyze the NAD(P)(H)-dependent interconversion of alcohols to aldehydes or ketones. ADH-like proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and generally have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. The active site zinc is coordinated by a histidine, two cysteines, and a water molecule. The second zinc seems to play a structural role, affects subunit interactions, and is typically coordinated by 4 cysteines. Other MDR members have only a catalytic zinc, and some contain no coordinated zinc. Pssm-ID: 176178 [Multi-domain] Cd Length: 271 Bit Score: 37.69 E-value: 5.59e-03
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| ApbA | pfam02558 | Ketopantoate reductase PanE/ApbA; This is a family of 2-dehydropantoate 2-reductases also ... |
3-37 | 5.66e-03 | |||||
Ketopantoate reductase PanE/ApbA; This is a family of 2-dehydropantoate 2-reductases also known as ketopantoate reductases, EC:1.1.1.169. The reaction catalyzed by this enzyme is: (R)-pantoate + NADP(+) <=> 2-dehydropantoate + NADPH. AbpA catalyzes the NADPH reduction of ketopantoic acid to pantoic acid in the alternative pyrimidine biosynthetic (APB) pathway. ApbA and PanE are allelic. ApbA, the ketopantoate reductase enzyme is required for the synthesis of thiamine via the APB biosynthetic pathway. Pssm-ID: 426831 [Multi-domain] Cd Length: 147 Bit Score: 36.44 E-value: 5.66e-03
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| AdhP | COG1064 | D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family [Carbohydrate transport ... |
2-49 | 5.75e-03 | |||||
D-arabinose 1-dehydrogenase, Zn-dependent alcohol dehydrogenase family [Carbohydrate transport and metabolism]; Pssm-ID: 440684 [Multi-domain] Cd Length: 332 Bit Score: 37.78 E-value: 5.75e-03
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| PRK07233 | PRK07233 | hypothetical protein; Provisional |
2-35 | 6.24e-03 | |||||
hypothetical protein; Provisional Pssm-ID: 235977 [Multi-domain] Cd Length: 434 Bit Score: 37.94 E-value: 6.24e-03
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| LDH | cd12186 | D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding ... |
1-35 | 6.42e-03 | |||||
D-Lactate dehydrogenase and D-2-Hydroxyisocaproic acid dehydrogenase (D-HicDH), NAD-binding and catalytic domains; D-Lactate dehydrogenase (LDH) catalyzes the interconversion of pyruvate and lactate, and is a member of the 2-hydroxyacid dehydrogenases family. LDH is homologous to D-2-hydroxyisocaproic acid dehydrogenase(D-HicDH) and shares the 2 domain structure of formate dehydrogenase. D-HicDH is a NAD-dependent member of the hydroxycarboxylate dehydrogenase family, and shares the Rossmann fold typical of many NAD binding proteins. HicDH from Lactobacillus casei forms a monomer and catalyzes the reaction R-CO-COO(-) + NADH + H+ to R-COH-COO(-) + NAD+. D-HicDH, like the structurally distinct L-HicDH, exhibits low side-chain R specificity, accepting a wide range of 2-oxocarboxylic acid side chains. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Pssm-ID: 240662 Cd Length: 329 Bit Score: 37.52 E-value: 6.42e-03
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| hydroxyacyl_CoA_DH | cd08254 | 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase, ... |
1-49 | 6.55e-03 | |||||
6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase, N-benzyl-3-pyrrolidinol dehydrogenase, and other MDR family members; This group contains enzymes of the zinc-dependent alcohol dehydrogenase family, including members (aka MDR) identified as 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase and N-benzyl-3-pyrrolidinol dehydrogenase. 6-hydroxycyclohex-1-ene-1-carboxyl-CoA dehydrogenase catalyzes the conversion of 6-Hydroxycyclohex-1-enecarbonyl-CoA and NAD+ to 6-Ketoxycyclohex-1-ene-1-carboxyl-CoA,NADH, and H+. This group displays the characteristic catalytic and structural zinc sites of the zinc-dependent alcohol dehydrogenases. NAD(P)(H)-dependent oxidoreductases are the major enzymes in the interconversion of alcohols and aldehydes, or ketones. Alcohol dehydrogenase in the liver converts ethanol and NAD+ to acetaldehyde and NADH, while in yeast and some other microorganisms ADH catalyzes the conversion acetaldehyde to ethanol in alcoholic fermentation. ADH is a member of the medium chain alcohol dehydrogenase family (MDR), which have a NAD(P)(H)-binding domain in a Rossmann fold of a beta-alpha form. The NAD(H)-binding region is comprised of 2 structurally similar halves, each of which contacts a mononucleotide. A GxGxxG motif after the first mononucleotide contact half allows the close contact of the coenzyme with the ADH backbone. The N-terminal catalytic domain has a distant homology to GroES. These proteins typically form dimers (typically higher plants, mammals) or tetramers (yeast, bacteria), and have 2 tightly bound zinc atoms per subunit, a catalytic zinc at the active site and a structural zinc in a lobe of the catalytic domain. NAD(H)-binding occurs in the cleft between the catalytic and coenzyme-binding domains at the active site, and coenzyme binding induces a conformational closing of this cleft. Coenzyme binding typically precedes and contributes to substrate binding. In human ADH catalysis, the zinc ion helps coordinate the alcohol, followed by deprotonation of a histidine, the ribose of NAD, a serine, then the alcohol, which allows the transfer of a hydride to NAD+, creating NADH and a zinc-bound aldehyde or ketone. In yeast and some bacteria, the active site zinc binds an aldehyde, polarizing it, and leading to the reverse reaction. Pssm-ID: 176216 [Multi-domain] Cd Length: 338 Bit Score: 37.61 E-value: 6.55e-03
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| YdfG | COG4221 | NADP-dependent 3-hydroxy acid dehydrogenase YdfG [Energy production and conversion]; ... |
2-57 | 7.03e-03 | |||||
NADP-dependent 3-hydroxy acid dehydrogenase YdfG [Energy production and conversion]; NADP-dependent 3-hydroxy acid dehydrogenase YdfG is part of the Pathway/BioSystem: Pyrimidine degradation Pssm-ID: 443365 [Multi-domain] Cd Length: 240 Bit Score: 37.08 E-value: 7.03e-03
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| NDP-sugDHase | TIGR03026 | nucleotide sugar dehydrogenase; Enzymes in this family catalyze the NAD-dependent ... |
1-38 | 9.03e-03 | |||||
nucleotide sugar dehydrogenase; Enzymes in this family catalyze the NAD-dependent alcohol-to-acid oxidation of nucleotide-linked sugars. Examples include UDP-glucose 6-dehydrogenase (1.1.1.22), GDP-mannose 6-dehydrogenase (1.1.1.132), UDP-N-acetylglucosamine 6-dehydrogenase (1.1.1.136), UDP-N-acetyl-D-galactosaminuronic acid dehydrogenase, and UDP-N-acetyl-D-mannosaminuronic acid dehydrogenase. These enzymes are most often involved in the biosynthesis of polysaccharides and are often found in operons devoted to that purpose. All of these enzymes contain three Pfam domains, pfam03721, pfam00984, and pfam03720 for the N-terminal, central, and C-terminal regions respectively. Pssm-ID: 274399 [Multi-domain] Cd Length: 409 Bit Score: 37.21 E-value: 9.03e-03
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| PGDH_4 | cd12173 | Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate ... |
3-42 | 9.23e-03 | |||||
Phosphoglycerate dehydrogenases, NAD-binding and catalytic domains; Phosphoglycerate dehydrogenases (PGDHs) catalyze the initial step in the biosynthesis of L-serine from D-3-phosphoglycerate. PGDHs come in 3 distinct structural forms, with this first group being related to 2-hydroxy acid dehydrogenases, sharing structural similarity to formate and glycerate dehydrogenases. PGDH in E. coli and Mycobacterium tuberculosis form tetramers, with subunits containing a Rossmann-fold NAD binding domain. Formate/glycerate and related dehydrogenases of the D-specific 2-hydroxyacid dehydrogenase superfamily include groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-adenosylhomocysteine hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. Pssm-ID: 240650 [Multi-domain] Cd Length: 304 Bit Score: 37.01 E-value: 9.23e-03
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| HPPR | cd12156 | Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; ... |
1-35 | 9.76e-03 | |||||
Hydroxy(phenyl)pyruvate Reductase, D-isomer-specific 2-hydroxyacid-related dehydrogenase; Hydroxy(phenyl)pyruvate reductase (HPPR) catalyzes the NADP-dependent reduction of hydroxyphenylpyruvates, hydroxypyruvate, or pyruvate to its respective lactate. HPPR acts as a dimer and is related to D-isomer-specific 2-hydroxyacid dehydrogenases, a superfamily that includes groups such as formate dehydrogenase, glycerate dehydrogenase, L-alanine dehydrogenase, and S-Adenosylhomocysteine Hydrolase. Despite often low sequence identity, these proteins typically have a characteristic arrangement of 2 similar subdomains of the alpha/beta Rossmann fold NAD+ binding form. The NAD+ binding domain is inserted within the linear sequence of the mostly N-terminal catalytic domain, which has a similar domain structure to the internal NAD binding domain. Structurally, these domains are connected by extended alpha helices and create a cleft in which NAD is bound, primarily to the C-terminal portion of the 2nd (internal) domain. Some related proteins have similar structural subdomain but with a tandem arrangement of the catalytic and NAD-binding subdomains in the linear sequence. While many members of this family are dimeric, alanine DH is hexameric and phosphoglycerate DH is tetrameric. Pssm-ID: 240633 [Multi-domain] Cd Length: 301 Bit Score: 37.06 E-value: 9.76e-03
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