Protein Info for GFF3313 in Xanthobacter sp. DMC5
Annotation: L-arabonate dehydratase
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: 50% identical to ARADA_AZOBR: L-arabonate dehydratase (araC) from Azospirillum brasilense
KEGG orthology group: K01687, dihydroxy-acid dehydratase [EC: 4.2.1.9] (inferred from 85% identity to sno:Snov_1919)Predicted SEED Role
"Dihydroxy-acid dehydratase (EC 4.2.1.9)" in subsystem Branched-Chain Amino Acid Biosynthesis (EC 4.2.1.9)
MetaCyc Pathways
- superpathway of branched chain amino acid biosynthesis (17/17 steps found)
- superpathway of L-isoleucine biosynthesis I (13/13 steps found)
- L-isoleucine biosynthesis I (from threonine) (7/7 steps found)
- L-valine biosynthesis (4/4 steps found)
- pyruvate fermentation to isobutanol (engineered) (4/5 steps found)
- L-isoleucine biosynthesis IV (4/6 steps found)
- L-isoleucine biosynthesis II (5/8 steps found)
- L-isoleucine biosynthesis III (4/7 steps found)
- superpathway of L-threonine metabolism (11/18 steps found)
KEGG Metabolic Maps
- Biosynthesis of alkaloids derived from histidine and purine
- Pantothenate and CoA biosynthesis
- Valine, leucine and isoleucine biosynthesis
Isozymes
Compare fitness of predicted isozymes for: 4.2.1.9
Use Curated BLAST to search for 4.2.1.9
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 (573 amino acids)
>GFF3313 L-arabonate dehydratase (Xanthobacter sp. DMC5) MIGTGKARMARGLRKGLTSYGDDGFALFLRKAFIKAMGYSDDALDRPIVGITNTYSDYNP CHGNAPQLIEAVKRGVMLAGAMPMVFPTISIHESFAHPTSMFLRNLMAMDTEEMIRAQPM DAVVVIGGCDKTLPAQIMAAASVDLPTVVVPVGPMVVGHHRGEVLGACTDCRRLWSAHRA GEIDEVEIDTVNGRLAPSVGTCMVMGTASTMACITETLGLSLPMSASIPAPHAERVRLAE QSGKVAARLAVEGGPRPSELLTPAAFHNALVVMQAIGGSTNGIIHLTAIANRAGVRLELE TLDAIGREVPVLVDLKPSGAHYMEHFHHAGGVPKLLKQLGDLIDLDAPTVSGGTLRELVE AAEEVPGQDVIRPRSQPIKAQGSMVVLRGNLAPGGAVLKQAAASERLLQHTGRAVVFDSV ADMAARIDDPDLDVTADDVLVLRNTGPKGAPGMPEAGYLPIPKKLGRQGVKDMVRISDAR MSGTAFGTIVLHITPESAVGGPLALVESGDMIRLDVEGRRIDLLVAEDELARRRAALADV PERPLPERGYARLFQQTVLQADEGCDFDFMVPR