Protein Info for GFF3897 in Variovorax sp. SCN45
Annotation: Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1)
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
Best Hits
Swiss-Prot: 54% identical to SDHA_RICCN: Succinate dehydrogenase flavoprotein subunit (sdhA) from Rickettsia conorii (strain ATCC VR-613 / Malish 7)
KEGG orthology group: K00239, succinate dehydrogenase flavoprotein subunit [EC: 1.3.99.1] (inferred from 98% identity to vpe:Varpa_1572)MetaCyc: 54% identical to succinate dehydrogenase flavoprotein subunit (Pseudomonas putida KT2440)
Succinate dehydrogenase (ubiquinone). [EC: 1.3.5.1]
Predicted SEED Role
"Succinate dehydrogenase flavoprotein subunit (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 (24/26 steps found)
- superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle (20/22 steps found)
- TCA cycle II (plants and fungi) (9/9 steps found)
- TCA cycle V (2-oxoglutarate synthase) (9/9 steps found)
- superpathway of glyoxylate bypass and TCA (11/12 steps found)
- TCA cycle I (prokaryotic) (9/10 steps found)
- TCA cycle III (animals) (9/10 steps found)
- TCA cycle VIII (Chlamydia) (6/6 steps found)
- TCA cycle IV (2-oxoglutarate decarboxylase) (8/9 steps found)
- partial TCA cycle (obligate autotrophs) (7/8 steps found)
- superpathway of glyoxylate cycle and fatty acid degradation (11/14 steps found)
- superpathway of anaerobic energy metabolism (invertebrates) (13/17 steps found)
- succinate to cytochrome bd oxidase electron transfer (2/2 steps found)
- succinate to cytochrome bo oxidase electron transfer (2/2 steps found)
- TCA cycle VI (Helicobacter) (7/9 steps found)
- TCA cycle VII (acetate-producers) (7/9 steps found)
- aerobic respiration I (cytochrome c) (3/4 steps found)
- aerobic respiration III (alternative oxidase pathway) (2/3 steps found)
- glycerol-3-phosphate to fumarate electron transfer (1/2 steps found)
- mixed acid fermentation (11/16 steps found)
- aerobic respiration II (cytochrome c) (yeast) (2/4 steps found)
- reductive TCA cycle I (7/11 steps found)
- incomplete reductive TCA cycle (4/7 steps found)
- pyruvate fermentation to propanoate I (4/7 steps found)
- anaerobic energy metabolism (invertebrates, mitochondrial) (6/10 steps found)
- reductive TCA cycle II (7/12 steps found)
- methylaspartate cycle (12/19 steps found)
- (S)-lactate fermentation to propanoate, acetate and hydrogen (7/13 steps found)
- L-glutamate degradation VIII (to propanoate) (4/11 steps found)
- Methanobacterium thermoautotrophicum biosynthetic metabolism (22/56 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
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Predict protein localization: PSORTb (Gram-negative bacteria)
Predict transmembrane helices and signal peptides: Phobius
Check the current SEED with FIGfam search
Find homologs in fast.genomics or the ENIGMA genome browser
Find the best match in UniProt
Protein Sequence (602 amino acids)
>GFF3897 Succinate dehydrogenase flavoprotein subunit (EC 1.3.5.1) (Variovorax sp. SCN45) MTYTKEKITKRKFDVVIVGAGGSGMRASLQLARAGLNVAVLSKVFPTRSHTVAAQGGVGA SLGNMSEDNWHYHFYDTIKGSDWLGDQDAIEFMCREAPKVVYELEHFGMPFDRNPDGTIY QRPFGGHTANYGEKPVQRACAAADRTGHAMLHTLYQKNVEARTQFFVEWMALDLIRDEEG DVVGVTALEMETGDLHILQAKTVLLATGGAGRIFQASTNAFINTGDGLGMAARSGIPLQD MEFWQFHPTGVAGAGVLLTEGCRGEGAILLNSNGERFMERYAPTLKDLAPRDFVSRSMDQ EIKEGRGCGPNKDYVLLKLDHLGADTIHKRLPSVYEIGVNFANVDITKEPIPVVPTIHYQ MGGIPTNIHGQVVVQKGEDNSAVVNGLYAVGECSCVSVHGANRLGTNSLLDLLVFGRAAG NHIVEFADKLKEHKPLPNDAADRTLERLNRLEATTGGEYAQDVAGEIRAVMQQHAAVFRK QASMDEGVVKIAAVRERVKAIGLKDKSKVFNTARIEALEVDNLIEVAQATMVSAAARKEC RGAHTVEDYERPADDPVAPLGRDDANWMKHTLWYSDDNRLSYKPVKLQPLTVASVPPKVR TF