Protein Info for GFF4356 in Xanthobacter sp. DMC5
Annotation: D-3-phosphoglycerate 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: 57% identical to SERA_HAEIN: D-3-phosphoglycerate dehydrogenase (serA) from Haemophilus influenzae (strain ATCC 51907 / DSM 11121 / KW20 / Rd)
KEGG orthology group: K00058, D-3-phosphoglycerate dehydrogenase [EC: 1.1.1.95] (inferred from 85% identity to xau:Xaut_3822)MetaCyc: 57% identical to phosphoglycerate dehydrogenase (Escherichia coli K-12 substr. MG1655)
Phosphoglycerate dehydrogenase. [EC: 1.1.1.95]; KETOGLUTREDUCT-RXN [EC: 1.1.1.95, 1.1.1.399]; 1.1.1.399 [EC: 1.1.1.95, 1.1.1.399]
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-cysteine biosynthesis IX (Trichomonas vaginalis) (2/3 steps found)
- L-glutamate degradation V (via hydroxyglutarate) (6/10 steps found)
- L-glutamate degradation XI (reductive Stickland reaction) (3/7 steps found)
KEGG Metabolic Maps
Isozymes
Compare fitness of predicted isozymes for: 1.1.1.95
Use Curated BLAST to search for 1.1.1.399 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 (419 amino acids)
>GFF4356 D-3-phosphoglycerate dehydrogenase (Xanthobacter sp. DMC5) VTQNAPHLSLSRDKIKVLLLEGVNDSAVEMMLAAGYTNLTRLPKALDGEALKEALKGVYL LGIRSRTQITADVLEAADRLIAIGCFSVGTNQVDIDATRIAGIPVFNAPFSNTRSVAELV IGEIVMLLRRIPNRSAAAHEGLWDKSATDSHEVRGKTLGIIGYGNIGSQLSNLAEAMGMR VIYYDHTDKLRHGNTEPVATMAEVLSQSDVVSLHVPETPATHGLIGRAEIAAMKKGAYLI NNSRGTVVDLDALADALKAGHLRGAAVDVFPVEPSANGQKFVSPLQGLANVILTPHIGGS TEEAQERIGAEVARKLLDYSDTGSTMGAVNFPQVQLPARPTGTRFIQVQRNLPGMLGRLN EVLARHAVNIAAQYYETNADIGYVVLDADASAVDSQAILSEIRALEGTIRARLLYEYKA