Protein Info for b0116 in Escherichia coli BW25113

Name: lpd
Annotation: dihydrolipoamide dehydrogenase (NCBI)

These analyses and tools can help you predict a protein's function, but be skeptical. For enzymes, over 10% of annotations from KEGG or SEED are probably incorrect. For other types of proteins, the error rates may be much higher. MetaCyc and Swiss-Prot have low error rates, but the best hits in these databases are often quite distant, so this protein's function may not be the same. TIGRFam has low error rates. Finally, many experimentally-characterized proteins are not in any of these databases. To find relevant papers, use PaperBLAST.

Protein Families and Features

• TIGR01350: dihydrolipoyl dehydrogenase
  • amino acids 7 to 460 (454 residues), 501.2 bits, E=1.3e-154
• PF01134: GIDA
  • amino acids 8 to 70 (63 residues), 29.6 bits, E=2e-10
• PF07992: Pyr_redox_2
  • amino acids 8 to 328 (321 residues), 224.8 bits, E=8.4e-70
• PF00890: FAD_binding_2
  • amino acids 9 to 42 (34 residues), 22.3 bits, see alignment (E = 3.5e-08)
• PF12831: FAD_oxidored
  • amino acids 9 to 45 (37 residues), 34.3 bits, 8.9e-12
• PF00070: Pyr_redox
  • amino acids 177 to 252 (76 residues), 61.8 bits, E=3.7e-20
• PF02852: Pyr_redox_dim
  • amino acids 347 to 455 (109 residues), 126.5 bits, E=2.6e-40

Best Hits

Swiss-Prot: 100% identical to DLDH_ECO57: Dihydrolipoyl dehydrogenase (lpdA) from Escherichia coli O157:H7

KEGG orthology group: K00382, dihydrolipoamide dehydrogenase [EC: 1.8.1.4] (inferred from 100% identity to eco:b0116)

MetaCyc: 100% identical to lipoamide dehydrogenase (Escherichia coli K-12 substr. MG1655)
1.97.1.-; Dihydrolipoyl dehydrogenase. [EC: 1.4.1.27, 1.8.1.4]; RXN-7716 [EC: 1.4.1.27, 1.8.1.4, 1.2.1.105]; RXN0-1132 [EC: 1.4.1.27, 1.8.1.4, 1.2.1.105, 1.2.1.104]; 1.8.1.4 [EC: 1.4.1.27, 1.8.1.4, 1.2.1.105, 1.2.1.104]; 1.4.1.27 [EC: 1.4.1.27, 1.8.1.4, 1.2.1.105, 1.2.1.104]; 1.2.1.105 [EC: 1.4.1.27, 1.8.1.4, 1.2.1.105, 1.2.1.104]; 1.2.1.104 [EC: 1.4.1.27, 1.8.1.4, 1.2.1.105, 1.2.1.104]

Predicted SEED Role

No annotation

MetaCyc Pathways

• superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (25/26 steps found)
• folate transformations III (E. coli) (9/9 steps found)
• superpathway of glyoxylate bypass and TCA (11/12 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (18/22 steps found)
• folate transformations II (plants) (10/11 steps found)
• TCA cycle I (prokaryotic) (9/10 steps found)
• pyruvate fermentation to acetate and (S)-lactate I (4/4 steps found)
• 2-oxoglutarate decarboxylation to succinyl-CoA (3/3 steps found)
• glycine biosynthesis II (3/3 steps found)
• glycine cleavage (3/3 steps found)
• glycine degradation (3/3 steps found)
• pyruvate decarboxylation to acetyl CoA I (3/3 steps found)
• pyruvate fermentation to acetate II (3/3 steps found)
• TCA cycle III (animals) (8/10 steps found)
• TCA cycle VIII (Chlamydia) (5/6 steps found)
• TCA cycle II (plants and fungi) (7/9 steps found)
• photosynthetic 3-hydroxybutanoate biosynthesis (engineered) (19/26 steps found)
• pyruvate fermentation to acetate V (2/3 steps found)
• anaerobic energy metabolism (invertebrates, mitochondrial) (7/10 steps found)
• superpathway of anaerobic energy metabolism (invertebrates) (12/17 steps found)
• folate transformations I (9/13 steps found)
• 1-butanol autotrophic biosynthesis (engineered) (19/27 steps found)
• reductive glycine pathway of autotrophic CO₂ fixation (6/9 steps found)
• 2-oxoisovalerate decarboxylation to isobutanoyl-CoA (1/3 steps found)
• photorespiration II (6/10 steps found)
• photorespiration I (5/9 steps found)
• photorespiration III (5/9 steps found)
• L-tryptophan degradation III (eukaryotic) (3/15 steps found)
• superpathway of L-lysine degradation (14/43 steps found)

KEGG Metabolic Maps

• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones
• Biosynthesis of terpenoids and steroids
• Citrate cycle (TCA cycle)
• Glycine, serine and threonine metabolism
• Glycolysis / Gluconeogenesis
• Pyruvate metabolism
• Valine, leucine and isoleucine degradation

Isozymes

Compare fitness of predicted isozymes for: 1.8.1.4

Use Curated BLAST to search for 1.2.1.104 or 1.2.1.105 or 1.4.1.27 or 1.8.1.4

Sequence Analysis Tools

See P0A9P0 at UniProt or InterPro

Protein Sequence (474 amino acids)

>b0116 dihydrolipoamide dehydrogenase (NCBI) (Escherichia coli BW25113)
MSTEIKTQVVVLGAGPAGYSAAFRCADLGLETVIVERYNTLGGVCLNVGCIPSKALLHVA
KVIEEAKALAEHGIVFGEPKTDIDKIRTWKEKVINQLTGGLAGMAKGRKVKVVNGLGKFT
GANTLEVEGENGKTVINFDNAIIAAGSRPIQLPFIPHEDPRIWDSTDALELKEVPERLLV
MGGGIIGLEMGTVYHALGSQIDVVEMFDQVIPAADKDIVKVFTKRISKKFNLMLETKVTA
VEAKEDGIYVTMEGKKAPAEPQRYDAVLVAIGRVPNGKNLDAGKAGVEVDDRGFIRVDKQ
LRTNVPHIFAIGDIVGQPMLAHKGVHEGHVAAEVIAGKKHYFDPKVIPSIAYTEPEVAWV
GLTEKEAKEKGISYETATFPWAASGRAIASDCADGMTKLIFDKESHRVIGGAIVGTNGGE
LLGEIGLAIEMGCDAEDIALTIHAHPTLHESVGLAAEVFEGSITDLPNPKAKKK