Protein Info for GFF2590 in Variovorax sp. SCN45
Annotation: Isocitrate dehydrogenase [NAD] (EC 1.1.1.41)
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: K00030, isocitrate dehydrogenase (NAD+) [EC: 1.1.1.41] (inferred from 91% identity to vap:Vapar_4079)Predicted SEED Role
"Isocitrate dehydrogenase [NAD] (EC 1.1.1.41)" in subsystem TCA Cycle (EC 1.1.1.41)
MetaCyc Pathways
- 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 III (animals) (9/10 steps found)
- nitrogen remobilization from senescing leaves (7/8 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 plant hormones
- Biosynthesis of terpenoids and steroids
- Citrate cycle (TCA cycle)
Isozymes
No predicted isozymesUse Curated BLAST to search for 1.1.1.41
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 (344 amino acids)
>GFF2590 Isocitrate dehydrogenase [NAD] (EC 1.1.1.41) (Variovorax sp. SCN45) MTSPRIPATLIPGDGIGPEIVDATLAAFDALGAPFEWDRQIAGLGGVVAAGDPLPLATLD SIRRTRLALKGPLETPSGGGYRSSNVRLREEFQLYANLRPALTIIPGGRFDKIDLVVVRE NLEGLYIGHEHYVPIDGDPHAVAMATGINTRQGSRRLLEYAFETAVATGRKKVTIVHKAN IMKALTGIFLETGLDLYEKKYKGKFELDTVIIDACAMKLVLNPWQFDMLVTTNLFGDILS DLVAGLVGGLGMAPGANIGADAAIFEAVHGSAPDIAGKGIANPTALLLAAALMLDHVRLP ELATRLRTAIDQTLNIDKVRTGDLGGTAGTEAFTKALVSRINGG