Protein Info for PGA1_c33950 in Phaeobacter inhibens DSM 17395

Annotation: diaminopimelate epimerase DapF

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: 52% identical to DAPF_RHOS4: Diaminopimelate epimerase (dapF) from Rhodobacter sphaeroides (strain ATCC 17023 / 2.4.1 / NCIB 8253 / DSM 158)

KEGG orthology group: K01778, diaminopimelate epimerase [EC: 5.1.1.7] (inferred from 82% identity to sit:TM1040_2809)

Predicted SEED Role

"Diaminopimelate epimerase (EC 5.1.1.7)" in subsystem Lysine Biosynthesis DAP Pathway (EC 5.1.1.7)

MetaCyc Pathways

aspartate superpathway (23/25 steps found)
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I (16/18 steps found)
L-lysine biosynthesis I (9/9 steps found)
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II (12/15 steps found)
L-lysine biosynthesis VI (6/7 steps found)
L-lysine biosynthesis II (7/9 steps found)

KEGG Metabolic Maps

Isozymes

No predicted isozymes

Use Curated BLAST to search for 5.1.1.7

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 I7DVD0 at UniProt or InterPro

Protein Sequence (281 amino acids)

>PGA1_c33950 diaminopimelate epimerase DapF (Phaeobacter inhibens DSM 17395)
MPEMTIGSDTRLPFMKMHGLGNDFVVVDARDQTWDITPAMAEGIAHRQMGIGFDQLTVIT
KGDEDAHLTFYNADGSTSAACGNATRCIARHLLDESGKTHLRLTTDRGLLLAEDAGNGLT
SVNMGEPQLDWQDIPLAEDVDTLELPIEGAPTATGMGNPHCTFFVDNAEVIPLAEFGARY
EHHPLYPERTNVQVAHVVAPDHLRMRVWERGVGITLASGSSSCATAVAAARRGLTSRKVQ
IDLDGGTLWIDWRKDGVWMTGPTMHVADGHFTRQFLESLSK