Protein Info for AMB_RS06915 in Magnetospirillum magneticum AMB-1
Annotation: squalene synthase HpnD
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
KEGG orthology group: K02291, phytoene synthase [EC: 2.5.1.32] (inferred from 100% identity to mag:amb1366)MetaCyc: 44% identical to presqualene diphosphate synthase (Rhodopseudomonas palustris BisB5)
Squalene synthase. [EC: 2.5.1.103, 2.5.1.21, 2.5.1.96]
Predicted SEED Role
"Phytoene synthase (EC 2.5.1.32)" in subsystem Carotenoids (EC 2.5.1.32)
MetaCyc Pathways
- epoxysqualene biosynthesis (2/3 steps found)
- neurosporene biosynthesis (2/5 steps found)
- trans-lycopene biosynthesis I (2/6 steps found)
- trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria) (3/8 steps found)
- β-carotene biosynthesis (engineered) (2/8 steps found)
- lycopadiene biosynthesis (1/7 steps found)
- 4,4'-diapolycopenedioate biosynthesis (1/9 steps found)
- botryococcenes and methylated squalene biosynthesis (1/9 steps found)
- staphyloxanthin biosynthesis (1/9 steps found)
- superpathway of ergosterol biosynthesis II (12/26 steps found)
- hopanoid biosynthesis (bacteria) (3/14 steps found)
- cholesterol biosynthesis I (2/16 steps found)
- cholesterol biosynthesis II (via 24,25-dihydrolanosterol) (2/16 steps found)
- cholesterol biosynthesis III (via desmosterol) (2/16 steps found)
- superpathway of carotenoid biosynthesis in plants (3/22 steps found)
- superpathway of ergosterol biosynthesis I (5/26 steps found)
- superpathway of cholesterol biosynthesis (5/38 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
- Biosynthesis of steroids
- Biosynthesis of terpenoids and steroids
- Carotenoid biosynthesis - General
Isozymes
Compare fitness of predicted isozymes for: 2.5.1.32
Use Curated BLAST to search for 2.5.1.103 or 2.5.1.21 or 2.5.1.32 or 2.5.1.96
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
See Q2W7K5 at UniProt or InterPro
Protein Sequence (286 amino acids)
>AMB_RS06915 squalene synthase HpnD (Magnetospirillum magneticum AMB-1) MTPSVLAIDPAQYDMVAEIVRASGSSFYWGMRLLDRPRRYAMYAIYAFCRVVDDIADEPG DPEVKRAQLAEWRVELDRLYAGAPTHAVAKALHGPVLQYNLPKEDFLAVIAGCESDAQPE VTRLSMAELELYCDRVACAVGRLSIRVFGPLRPKSIETANATGMALQLTNILRDVAVDAK IGRLYLPDELLSKHGIASRDPMEVLAHPNLVAVCRELGETARGYFLASDAGQAECSRADM RPATLMKEMYREIFTRVEAEGFVPRDPPVKVSKAFKLWCILRHGLL