Protein Info for GFF4404 in Xanthobacter sp. DMC5

Annotation: Dihydrolipoyl dehydrogenase 3

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 2 to 467 (466 residues), 560 bits, E=1.9e-172
• PF07992: Pyr_redox_2
  • amino acids 3 to 329 (327 residues), 249.1 bits, E=3e-77
• PF01134: GIDA
  • amino acids 4 to 146 (143 residues), 27.3 bits, E=9.1e-10
• PF00890: FAD_binding_2
  • amino acids 4 to 40 (37 residues), 26.1 bits, 2.2e-09
• PF12831: FAD_oxidored
  • amino acids 4 to 42 (39 residues), 30.1 bits, 1.4e-10
• PF13450: NAD_binding_8
  • amino acids 7 to 42 (36 residues), 24.8 bits, 9.9e-09
• PF13738: Pyr_redox_3
  • amino acids 132 to 313 (182 residues), 30.3 bits, E=1.2e-10
• PF00070: Pyr_redox
  • amino acids 176 to 252 (77 residues), 79.5 bits, E=1e-25
• PF02852: Pyr_redox_dim
  • amino acids 348 to 457 (110 residues), 145.9 bits, E=2.3e-46

Best Hits

Swiss-Prot: 60% identical to DLDH2_ARATH: Dihydrolipoyl dehydrogenase 2, mitochondrial (LPD2) from Arabidopsis thaliana

KEGG orthology group: K00382, dihydrolipoamide dehydrogenase [EC: 1.8.1.4] (inferred from 97% identity to xau:Xaut_0159)

MetaCyc: 59% identical to glycine cleavage system L protein 1 (Arabidopsis thaliana col)
GCVMULTI-RXN [EC: 1.4.1.27]

Predicted SEED Role

"Dihydrolipoamide dehydrogenase of 2-oxoglutarate dehydrogenase (EC 1.8.1.4)" in subsystem TCA Cycle (EC 1.8.1.4)

MetaCyc Pathways

• folate transformations III (E. coli) (9/9 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (18/22 steps found)
• folate transformations II (plants) (10/11 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)
• folate transformations I (10/13 steps found)
• photorespiration I (7/9 steps found)
• photorespiration III (7/9 steps found)
• 2-oxoisovalerate decarboxylation to isobutanoyl-CoA (2/3 steps found)
• photorespiration II (7/10 steps found)
• reductive glycine pathway of autotrophic CO₂ fixation (6/9 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 1.4.1.27 or 1.8.1.4

Protein Sequence (467 amino acids)

>GFF4404 Dihydrolipoyl dehydrogenase 3 (Xanthobacter sp. DMC5)
MSYDLTIIGTGPGGYVCAIRAAQLGLKVAVVEKRGTHGGTCLNVGCIPSKALLYASELFE
EAGHKFGEMGIGVPAPKLDLPAMLAFKDRGVDGNVKGVEFLLKKNKVDVYMGAGKILGPG
KVEVTLNADGKVEVLETKNIVIATGSDFAPLPGVTIDEERIVSSTGALKLPKVPGKLVVV
GAGVIGLELGSVWRRLGAQVTVVEFLDRILPGMDSDVAKSFQRILDKQGFTFKLGTKVTG
VDTKGKTLKVSVEPAAGGAAEVLEADVVLVAIGRIPYTAGLGLEEAGVAKDARGRVVTDH
HFATNVPGIYAIGDVIVGPMLAHKAEDEGVALAEQLAGKAGHVNYDVIPGVVYTFPEVAS
VGKTEDELKAAGVAYKVGKFPFTANGRTKVNNTTDGFVKIIADAATDKVLGAHIIGPEAG
EMIHECAVLMEFGGSSEDLARTCHAHPTRSEAVKEAAMAVEKRAIHM