Protein Info for AMB_RS03140 in Magnetospirillum magneticum AMB-1
Annotation: isocitrate dehydrogenase (NADP(+))
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: 77% identical to IDH_SPHYA: Isocitrate dehydrogenase [NADP] (icd) from Sphingobium yanoikuyae
KEGG orthology group: K00031, isocitrate dehydrogenase [EC: 1.1.1.42] (inferred from 100% identity to mag:amb0608)MetaCyc: 72% identical to isocitrate dehydrogenase subunit (Mycobacterium tuberculosis H37Rv)
Isocitrate dehydrogenase (NADP(+)). [EC: 1.1.1.42]
Predicted SEED Role
"Isocitrate dehydrogenase [NADP] (EC 1.1.1.42)" in subsystem TCA Cycle (EC 1.1.1.42)
MetaCyc Pathways
- TCA cycle V (2-oxoglutarate synthase) (9/9 steps found)
- TCA cycle I (prokaryotic) (9/10 steps found)
- TCA cycle VII (acetate-producers) (8/9 steps found)
- superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass (20/26 steps found)
- reductive TCA cycle I (9/11 steps found)
- TCA cycle IV (2-oxoglutarate decarboxylase) (7/9 steps found)
- superpathway of glyoxylate bypass and TCA (9/12 steps found)
- methylaspartate cycle (14/19 steps found)
- partial TCA cycle (obligate autotrophs) (6/8 steps found)
- ethene biosynthesis V (engineered) (18/25 steps found)
- TCA cycle VI (Helicobacter) (6/9 steps found)
- nitrogen remobilization from senescing leaves (5/8 steps found)
- cytosolic NADPH production (yeast) (2/5 steps found)
- mixed acid fermentation (9/16 steps found)
- superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) (3/8 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 phenylpropanoids
- Biosynthesis of plant hormones
- Biosynthesis of terpenoids and steroids
- Citrate cycle (TCA cycle)
- Glutathione metabolism
- Reductive carboxylate cycle (CO2 fixation)
Isozymes
Compare fitness of predicted isozymes for: 1.1.1.42
Use Curated BLAST to search for 1.1.1.42
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
See Q2W9R3 at UniProt or InterPro
Protein Sequence (406 amino acids)
>AMB_RS03140 isocitrate dehydrogenase (NADP(+)) (Magnetospirillum magneticum AMB-1) MNKIKVANPIVELDGDEMTRIIWKFIKDKLILPYLDVDLKYYDLGIEYRDKTDDKVTIEA SEAIKKYGVGVKCATITPDEARVKEFNLKKMWKSPNGTIRNILDGTVFREPIICKNVPRL VPGWTKPIVIGRHAFGDQYKATDFTVPGPGKLTIKFVGTNGETIEHEVFDFPGAGVAMGM YNLDESIYGFARACLNYGQQKKWPVYLSTKNTILKAYDGRFKDIFQEVYEKEFKAEYAKL GITYEHRLIDDMVASALKWSGEFVWACKNYDGDVQSDTVAQGFGSLGLMTSVLMSPDGKV VEAEAAHGTVTRHYREHQKGKETSTNPIASIFAWTRGLFYRAQFDNTPEVAKFAQALEEV CVETVESGFMTKDLAILIGPGQSWLTTQQFLDKLDENLKKRMGLAA