Protein Info for GFF2017 in Variovorax sp. SCN45

Annotation: D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95)

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: 46% identical to GHRA_SERP5: Glyoxylate/hydroxypyruvate reductase A (ghrA) from Serratia proteamaculans (strain 568)

KEGG orthology group: K12972, gyoxylate/hydroxypyruvate reductase A [EC: 1.1.1.79 1.1.1.81] (inferred from 94% identity to vpe:Varpa_5352)

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)
L-serine biosynthesis II (3/4 steps found)
L-cysteine biosynthesis IX (Trichomonas vaginalis) (2/3 steps found)
formaldehyde assimilation I (serine pathway) (9/13 steps found)

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.79, 1.1.1.81, 1.1.1.95

Use Curated BLAST to search for 1.1.1.79 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)

Search 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 (306 amino acids)

>GFF2017 D-3-phosphoglycerate dehydrogenase (EC 1.1.1.95) (Variovorax sp. SCN45)
MRITVYLTDNRPDPWIEGLKAELPDAVIEPWKPGAPQADHAVVWAPPQELIDEQPQLRGI
FNIGAGVDALLKLKVPAHTRIVRLDDAGMSVQMAEYVCHTLIRHFREFDAYEADAREGKW
SYRKPRMRRDFPVGIMGLGVLGERVAKAVAQFEFPVLGWSRSSKDIDGVQVFSGESQFDE
FLSSTRVLVNLLPLTEATRGILNRKTLGKLKPEGYLISIARGGHLVEDDLIPMLDAGQLA
GATLDVFQVEPLPADHAFWRHPKITVTPHGSARTLREESIAQIAGKIRAMEQGLPIAGVV
DPARGY