Protein Info for PS417_08890 in Pseudomonas simiae WCS417

Annotation: succinate dehydrogenase

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

• PF13085: Fer2_3
  • amino acids 3 to 108 (106 residues), 108.1 bits, E=4.5e-35
• TIGR00384: succinate dehydrogenase and fumarate reductase iron-sulfur protein
  • amino acids 6 to 226 (221 residues), 277.7 bits, E=3.1e-87
• PF13183: Fer4_8
  • amino acids 142 to 216 (75 residues), 39.3 bits, E=1.5e-13
• PF13237: Fer4_10
  • amino acids 144 to 213 (70 residues), 35.3 bits, E=1.9e-12
• PF13534: Fer4_17
  • amino acids 144 to 217 (74 residues), 37.6 bits, E=5.1e-13

Best Hits

Swiss-Prot: 70% identical to SDHB_ECOLI: Succinate dehydrogenase iron-sulfur subunit (sdhB) from Escherichia coli (strain K12)

KEGG orthology group: K00240, succinate dehydrogenase iron-sulfur protein [EC: 1.3.99.1] (inferred from 99% identity to pba:PSEBR_a4141)

MetaCyc: 93% identical to succinate dehydrogenase iron-sulfur subunit (Pseudomonas putida KT2440)
Succinate dehydrogenase (ubiquinone). [EC: 1.3.5.1]

Predicted SEED Role

"Succinate dehydrogenase iron-sulfur protein (EC 1.3.99.1)" in subsystem Serine-glyoxylate cycle or Succinate dehydrogenase or TCA Cycle (EC 1.3.99.1)

MetaCyc Pathways

• superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (22/26 steps found)
• superpathway of glyoxylate bypass and TCA (11/12 steps found)
• partial TCA cycle (obligate autotrophs) (8/8 steps found)
• superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (18/22 steps found)
• TCA cycle I (prokaryotic) (9/10 steps found)
• superpathway of glyoxylate cycle and fatty acid degradation (11/14 steps found)
• aerobic respiration III (alternative oxidase pathway) (3/3 steps found)
• TCA cycle VIII (Chlamydia) (5/6 steps found)
• succinate to cytochrome bo oxidase electron transfer (2/2 steps found)
• TCA cycle II (plants and fungi) (7/9 steps found)
• TCA cycle V (2-oxoglutarate synthase) (7/9 steps found)
• TCA cycle VI (Helicobacter) (7/9 steps found)
• TCA cycle VII (acetate-producers) (7/9 steps found)
• mixed acid fermentation (12/16 steps found)
• aerobic respiration I (cytochrome c) (3/4 steps found)
• aerobic respiration II (cytochrome c) (yeast) (3/4 steps found)
• TCA cycle III (animals) (7/10 steps found)
• glycerol-3-phosphate to fumarate electron transfer (1/2 steps found)
• succinate to cytochrome bd oxidase electron transfer (1/2 steps found)
• TCA cycle IV (2-oxoglutarate decarboxylase) (6/9 steps found)
• reductive TCA cycle I (6/11 steps found)
• incomplete reductive TCA cycle (3/7 steps found)
• anaerobic energy metabolism (invertebrates, mitochondrial) (5/10 steps found)
• pyruvate fermentation to propanoate I (2/7 steps found)
• superpathway of anaerobic energy metabolism (invertebrates) (9/17 steps found)
• reductive TCA cycle II (5/12 steps found)
• methylaspartate cycle (10/19 steps found)
• (S)-lactate fermentation to propanoate, acetate and hydrogen (5/13 steps found)
• L-glutamate degradation VIII (to propanoate) (2/11 steps found)
• Methanobacterium thermoautotrophicum biosynthetic metabolism (20/56 steps found)

KEGG Metabolic Maps

• Benzoate degradation via CoA ligation
• 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
• Butanoate metabolism
• Citrate cycle (TCA cycle)
• Oxidative phosphorylation
• Reductive carboxylate cycle (CO2 fixation)

Isozymes

Compare fitness of predicted isozymes for: 1.3.99.1

Use Curated BLAST to search for 1.3.5.1 or 1.3.99.1

Sequence Analysis Tools

See A0A1N7U487 at UniProt or InterPro

Protein Sequence (234 amino acids)

>PS417_08890 succinate dehydrogenase (Pseudomonas simiae WCS417)
MLKVSVYRYNPDQDAAPFMQEFQVDTGGKDLMVLDVLALIKEQDEGFSYRRSCREGVCGS
DGMNINGKNGLACITPLSAVVKGNKLIVRPLPGLPVIRDLVVDMSIFYKQYEKVKPFLQN
DTPAPAIERLQSPEEREKLDGLYECILCACCSTSCPSFWWNPDKFLGPAALLQAYRFLAD
SRDTKTSERLASLDDPFSVFRCRGIMNCVNVCPKGLNPTKAIGHIRNMLLQSGV