Protein Info for GFF5702 in Variovorax sp. SCN45
Annotation: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.7.4)
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: 86% identical to ISPH_POLSJ: 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (ispH) from Polaromonas sp. (strain JS666 / ATCC BAA-500)
KEGG orthology group: K03527, 4-hydroxy-3-methylbut-2-enyl diphosphate reductase [EC: 1.17.1.2] (inferred from 96% identity to vpe:Varpa_4693)MetaCyc: 56% identical to 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (Escherichia coli K-12 substr. MG1655)
RXN-24043 [EC: 1.17.7.4]; 1.17.7.4 [EC: 1.17.7.4]
Predicted SEED Role
"4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.1.2)" in subsystem Isoprenoid Biosynthesis or polyprenyl synthesis (EC 1.17.1.2)
MetaCyc Pathways
- methylerythritol phosphate pathway II (8/9 steps found)
- superpathway of geranylgeranyl diphosphate biosynthesis II (via MEP) (10/12 steps found)
- taxadiene biosynthesis (engineered) (10/13 steps found)
- methylerythritol phosphate pathway I (7/9 steps found)
- isoprene biosynthesis I (7/10 steps found)
- superpathway of ergosterol biosynthesis II (11/26 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from terpenoid and polyketide
- Biosynthesis of plant hormones
- Biosynthesis of terpenoids and steroids
- Terpenoid biosynthesis
Isozymes
Compare fitness of predicted isozymes for: 1.17.1.2
Use Curated BLAST to search for 1.17.1.2 or 1.17.7.4
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
Compare to protein structures
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 (322 amino acids)
>GFF5702 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (EC 1.17.7.4) (Variovorax sp. SCN45) MNTGISEVILAEPRGFCAGVDRAIEIVERAIAKFGAPIYVRHEIVHNTYVVNELKAKGAI FIEELSDVPPGATLVFSAHGVSKAVEQEARDRGFEIFDATCPLVTKVHVEVAKLAKEGYE FIMIGHKGHPEVEGTMGQLSSGIHLVEDVADVAKVAPAQTDKLAVVTQTTLSVDDAAEIA AAVRARFPAVREPKQQDICYATQNRQDAVKIMSPQVDLVIVVGSPTSSNSNRLRELAQRL GTESYMVDSAEELKPEWFEGKTRIGLTAGASAPEVLVREVIDRVRALGAVSVRKMDGIEE TIKFPLPKGLKLDDIPPPGHIS