Protein Info for GFF2853 in Xanthobacter sp. DMC5

Annotation: Glycerate dehydrogenase

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: 49% identical to DHGY_METEA: Glycerate dehydrogenase (hprA) from Methylobacterium extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)

KEGG orthology group: K00018, glycerate dehydrogenase [EC: 1.1.1.29] (inferred from 52% identity to atu:Atu5333)

MetaCyc: 49% identical to hydroxypyruvate reductase subunit (Methylorubrum extorquens AM1)
Hydroxypyruvate reductase. [EC: 1.1.1.81]; 1.1.1.81 [EC: 1.1.1.81]

Predicted SEED Role

"D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)" in subsystem Glycine and Serine Utilization or Pyridoxin (Vitamin B6) Biosynthesis or Serine Biosynthesis (EC 1.1.1.95)

MetaCyc Pathways

superpathway of sulfate assimilation and cysteine biosynthesis (9/9 steps found)
superpathway of L-serine and glycine biosynthesis I (4/4 steps found)
L-serine biosynthesis I (3/3 steps found)
photorespiration I (7/9 steps found)
photorespiration III (7/9 steps found)
L-cysteine biosynthesis IX (Trichomonas vaginalis) (2/3 steps found)
photorespiration II (7/10 steps found)
L-serine biosynthesis II (1/4 steps found)
formaldehyde assimilation I (serine pathway) (7/13 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.81, 1.1.1.95

Use Curated BLAST to search for 1.1.1.29 or 1.1.1.81 or 1.1.1.95

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 (319 amino acids)

>GFF2853 Glycerate dehydrogenase (Xanthobacter sp. DMC5)
MHKIVVLDRDTIAPEVQVRRPSFAHEWVEYARTSPSEVVARAKDATIIINNKVDLRADTL
AQLPQLKLIAIAATGTDCVDKTAAAAQGVPTVNIRGYAKATVPEHTFALLLSLARSIVPY
RQEVLEGAWQAAQQFCFFTNPIVDLAGRRLGIVGAGVLGSQVAGIARAFGMDVVFYDPMA
KPGTAGVVSLDELIETSHAITLHCPLTDETRGMFDMAAFRRMKNRPILINTARGGLIVEE
DLEVALDEGLVSAAGLDVTLPEPPAPDSAFMRLARRRNVICTPHIAWASLEAQQALADQL
IDNVENFVAGQPTNVVSPD