Protein Info for GFF292 in Xanthobacter sp. DMC5
Annotation: Isopentenyl-diphosphate delta-isomerase
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: 87% identical to GLXD_RHIME: Glutamate synthase large subunit-like protein (glxD) from Rhizobium meliloti (strain 1021)
KEGG orthology group: None (inferred from 95% identity to xau:Xaut_4697)Predicted SEED Role
"Glutamate synthase [NADPH] large chain (EC 1.4.1.13)" in subsystem Ammonia assimilation or Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis (EC 1.4.1.13)
MetaCyc Pathways
- L-asparagine biosynthesis III (tRNA-dependent) (4/4 steps found)
- glutaminyl-tRNAgln biosynthesis via transamidation (4/4 steps found)
- ammonia assimilation cycle III (3/3 steps found)
- L-glutamate biosynthesis I (2/2 steps found)
- L-glutamine degradation I (1/1 steps found)
- L-glutamine degradation II (1/1 steps found)
- L-citrulline biosynthesis (6/8 steps found)
- L-glutamate and L-glutamine biosynthesis (5/7 steps found)
- superpathway of L-citrulline metabolism (8/12 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
- Glutamate metabolism
- Nitrogen metabolism
Isozymes
Compare fitness of predicted isozymes for: 1.4.1.13
Use Curated BLAST to search for 1.4.1.13
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 (445 amino acids)
>GFF292 Isopentenyl-diphosphate delta-isomerase (Xanthobacter sp. DMC5) MTAHNNTPRTPPRFSSTFDPATLAEIRRAAATGIYDIRGGGTKRKLPHFDDLLFLGASMS RYPLEGYREKCGTEVTLGTRFAKKPITLKTPVTIAGMSFGALSAQAKEALGRGASTVGTS TTTGDGGMTPEERGQSKTLVYQYLPSRYGMNPVDLRKADAIEIVIGQGAKPGGGGMLLGQ KISDRVAAMRTLPKGIDQRSACRHPDWTGPDDLEIKIEELREITDWEKPIYVKVGASRPY YDTALAVKAGADVVVLDGMQGGTAATQDVFIEHVGIPILAAIRPAVQALQDLDMHRKVQL IVSGGIRTGADVAKALALGADAVAIGTAALVALGDNDPQWEDEYQALGSTAGAYDDWHEG RDPAGITTQDPELSKRLDPVKAGRRLANYLSVMTLEAQTIARACGKSHLHNLEPEDLVAL TVEAAAMAGVPLAGTTWVPGKTGGY