Protein Info for SO0426 in Shewanella oneidensis MR-1

Name: lpdA
Annotation: pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI ptt file)

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 459 (453 residues), 495.7 bits, E=6e-153
• PF01134: GIDA
  • amino acids 8 to 69 (62 residues), 27.4 bits, E=7.2e-10
• PF07992: Pyr_redox_2
  • amino acids 8 to 329 (322 residues), 225 bits, E=5.6e-70
• PF12831: FAD_oxidored
  • amino acids 8 to 46 (39 residues), 33.4 bits, 1.3e-11
• PF00890: FAD_binding_2
  • amino acids 9 to 42 (34 residues), 21.8 bits, see alignment (E = 3.9e-08)
• PF00070: Pyr_redox
  • amino acids 178 to 251 (74 residues), 59.2 bits, E=1.8e-19
• PF02852: Pyr_redox_dim
  • amino acids 348 to 456 (109 residues), 127.8 bits, E=8.4e-41

Best Hits

Swiss-Prot: 86% identical to DLDH_SHIFL: Dihydrolipoyl dehydrogenase (lpdA) from Shigella flexneri

KEGG orthology group: K00382, dihydrolipoamide dehydrogenase [EC: 1.8.1.4] (inferred from 100% identity to shn:Shewana3_0428)

MetaCyc: 86% 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

"Dihydrolipoamide dehydrogenase of pyruvate dehydrogenase complex (EC 1.8.1.4) @ Dihydrolipoamide dehydrogenase (EC 1.8.1.4)" (EC 1.8.1.4)

MetaCyc Pathways

• superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (22/26 steps found)
• folate transformations II (plants) (11/11 steps found)
• folate transformations III (E. coli) (9/9 steps found)
• photosynthetic 3-hydroxybutanoate biosynthesis (engineered) (21/26 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (18/22 steps found)
• TCA cycle III (animals) (9/10 steps found)
• 1-butanol autotrophic biosynthesis (engineered) (21/27 steps found)
• TCA cycle II (plants and fungi) (8/9 steps found)
• superpathway of glyoxylate bypass and TCA (10/12 steps found)
• 2-oxoglutarate decarboxylation to succinyl-CoA (3/3 steps found)
• 2-oxoisovalerate decarboxylation to isobutanoyl-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 I (prokaryotic) (8/10 steps found)
• photorespiration II (8/10 steps found)
• TCA cycle VIII (Chlamydia) (5/6 steps found)
• folate transformations I (10/13 steps found)
• photorespiration I (7/9 steps found)
• photorespiration III (7/9 steps found)
• pyruvate fermentation to acetate and (S)-lactate I (3/4 steps found)
• pyruvate fermentation to acetate V (2/3 steps found)
• reductive glycine pathway of autotrophic CO₂ fixation (6/9 steps found)
• anaerobic energy metabolism (invertebrates, mitochondrial) (5/10 steps found)
• superpathway of anaerobic energy metabolism (invertebrates) (10/17 steps found)
• L-tryptophan degradation III (eukaryotic) (3/15 steps found)
• superpathway of L-lysine degradation (8/43 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 Q8EJN7 at UniProt or InterPro

Protein Sequence (475 amino acids)

>SO0426 pyruvate dehydrogenase complex, E3 component, lipoamide dehydrogenase (NCBI ptt file) (Shewanella oneidensis MR-1)
MSNEIKTQVVVLGAGPAGYSAAFRAADLGLETVIVERFSTLGGVCLNVGCIPSKALLHVA
KVIEEAKAVAAHGVVFGEPTIDLDKLRSFKQKVISQLTGGLGGMSKMRKVNVVNGFGKFS
GPNSLEVTAEDGTVTVVKFDQAIIAAGSRPIKLPFIPHEDPRIWDSTDALELKEVPGKLL
VMGGGIIGLEMGTVYSSLGSEIDVVEMFDQVIPAADKDVVRVFTKQIKKKFNLILETKVT
AVEAREDGIYVSMEGKSAPAEPVRYDAVLVAIGRTPNGKLIDAEKAGVKIDERGFINVDK
QLRTNVPHIYAIGDIVGQPMLAHKGVHEGHVAAEVIAGMKHYFDPKVIPSIAYTDPEVAW
VGLTEKEAKEQGIAYETATFPWAASGRAIASDCSEGMTKLIFDKDTHRVIGGAIVGVNGG
ELLGEIGLAIEMGCDAEDLALTIHAHPTLHESVGLAAEIYEGSITDLPNPKAKKK