Protein Info for GFF4463 in Variovorax sp. SCN45

Annotation: alpha-methyl-L-serine aldolase

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

• PF00464: SHMT
  • amino acids 31 to 392 (362 residues), 150.8 bits, E=9.1e-48
• PF01212: Beta_elim_lyase
  • amino acids 86 to 327 (242 residues), 49.6 bits, E=7.4e-17
• PF01041: DegT_DnrJ_EryC1
  • amino acids 89 to 268 (180 residues), 34.5 bits, E=2.7e-12
• PF00155: Aminotran_1_2
  • amino acids 97 to 330 (234 residues), 39.9 bits, E=6.2e-14

Best Hits

Swiss-Prot: 35% identical to GLYA_SULTO: Serine hydroxymethyltransferase (glyA) from Sulfurisphaera tokodaii (strain DSM 16993 / JCM 10545 / NBRC 100140 / 7)

KEGG orthology group: K00600, glycine hydroxymethyltransferase [EC: 2.1.2.1] (inferred from 92% identity to vap:Vapar_0929)

Predicted SEED Role

"Serine hydroxymethyltransferase (EC 2.1.2.1)" in subsystem Folate Biosynthesis or Glycine Biosynthesis or Glycine and Serine Utilization or LMPTP YwlE cluster or Photorespiration (oxidative C2 cycle) or Serine-glyoxylate cycle or Serine Biosynthesis (EC 2.1.2.1)

MetaCyc Pathways

• folate transformations III (E. coli) (8/9 steps found)
• superpathway of L-serine and glycine biosynthesis I (4/4 steps found)
• folate transformations II (plants) (9/11 steps found)
• dTMP de novo biosynthesis (mitochondrial) (3/3 steps found)
• glycine degradation (3/3 steps found)
• folate polyglutamylation (4/5 steps found)
• glycine biosynthesis I (1/1 steps found)
• formaldehyde assimilation I (serine pathway) (9/13 steps found)
• photorespiration I (6/9 steps found)
• photorespiration III (6/9 steps found)
• glycine betaine degradation I (5/8 steps found)
• glycine betaine degradation III (4/7 steps found)
• photorespiration II (6/10 steps found)
• purine nucleobases degradation II (anaerobic) (16/24 steps found)
• folate transformations I (8/13 steps found)
• glycine betaine degradation II (mammalian) (1/4 steps found)

KEGG Metabolic Maps

• Cyanoamino acid metabolism
• Glycine, serine and threonine metabolism
• Methane metabolism
• One carbon pool by folate

Isozymes

Compare fitness of predicted isozymes for: 2.1.2.1

Use Curated BLAST to search for 2.1.2.1

Protein Sequence (422 amino acids)

>GFF4463 alpha-methyl-L-serine aldolase (Variovorax sp. SCN45)
MLSIAADASARDAAGVAAEIERLVADNHRIHDVDGLNLNPATNVMNPAAEALLSRGLGSR
PSLGYPGDKYEMGLEAIERIEVVAAELAAEVFGAKFAEVRVSSGALSNLYVFMATCQPGD
TIIAPPATIGGHVTHHAAGAAGLYGLKTVPAPVDADGYTVDVSALARLAREVKPKLITIG
GSLNLFPHPVPAIREIADSVGAKLLFDAAHLSGMVAGKAWPQPLEDGAHAITMSTYKSLG
GPAGGLIVSNDAALMERIDAIAYPGLTANSDAGRTAALARGLLDWKVHGKAYAAAMRETA
QALARALDAEGLPVFAKARGFTQSHQLAVEAARWGGGQRAAKLLAQGGLLACGIGLPIAP
VDGDINGLRLGVPEIVRLGFTADDMPQLASWIARALRGDGALVAAEVRERRKRLGELRYI
VR