Protein Info for PGA1_c29490 in Phaeobacter inhibens DSM 17395
Annotation: dihydroxy-acid dehydratase LivD
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: 92% identical to ILVD_RUEPO: Dihydroxy-acid dehydratase (ilvD) from Ruegeria pomeroyi (strain ATCC 700808 / DSM 15171 / DSS-3)
KEGG orthology group: K01687, dihydroxy-acid dehydratase [EC: 4.2.1.9] (inferred from 92% identity to sil:SPO3314)MetaCyc: 72% identical to dihydroxy-acid dehydratase (Escherichia coli K-12 substr. MG1655)
Dihydroxy-acid dehydratase. [EC: 4.2.1.9]; 4.2.1.9 [EC: 4.2.1.9]
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 (12/13 steps found)
- superpathway of L-threonine metabolism (15/18 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)
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
See I7F2J3 at UniProt or InterPro
Protein Sequence (614 amino acids)
>PGA1_c29490 dihydroxy-acid dehydratase LivD (Phaeobacter inhibens DSM 17395) MPMYRSRTSTHGRNMAGARGLWRATGMTDDDFGKPIIAIVNSFTQFVPGHVHLKDLGQMV AREVEAAGGVAKEFNTIAVDDGIAMGHDGMLYSLPSREVIADSVEYMVNAHCADAMVCIS NCDKITPGMLMAAMRLNIPAIFVSGGPMEAGKIDIADLDMKKIDLVDAMVAAASDTMTDE QVQHIEENACPTCGSCSGMFTANSMNCLAEALGLALPGNGSTLATHADRKHLFLEAGRKI VDITKRHYVGEEKGLLPREIATFDAFENAMSLDIAMGGSTNTVLHLLAIANEGKVDFTMT DMDRLSRKVPCLCKVAPNIENVHMEDVHRAGGIFSILGELSRAGLLHNECSTVHSSTMGE AIAKWDIKVANNPDAEALFKAAPGGVRTTEAFSQSNRYKELDTDREGGVIRSKDHAFSQD GGLAVLFGNIARDGCIVKTAGVDDNILKFTGSAYVCESQDQAVNDILTSKVKEGDVVVIR YEGPRGGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGTIG LVQQGDTIEIDIPNRTIHLAVSDEELAARRAAQDAAGWKPVKPRKRKVSTALKAYALLAT SAAKGAVRALPDDE