Protein Info for Pf1N1B4_2454 in Pseudomonas fluorescens FW300-N1B4

Updated annotation (from data): Serine hydroxymethyltransferase (EC 2.1.2.1)
Rationale: Specific phenotype: utilization of Carnitine (carnitine is broken down via glycine betaine and glycine)
Original annotation: Serine hydroxymethyltransferase (EC 2.1.2.1)

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 10 to 386 (377 residues), 580 bits, E=2e-178
• PF00155: Aminotran_1_2
  • amino acids 65 to 371 (307 residues), 29.7 bits, E=3.9e-11

Best Hits

Swiss-Prot: 99% identical to GLYA3_PSEPF: Serine hydroxymethyltransferase 3 (glyA3) from Pseudomonas fluorescens (strain Pf0-1)

KEGG orthology group: K00600, glycine hydroxymethyltransferase [EC: 2.1.2.1] (inferred from 99% identity to pfo:Pfl01_5208)

MetaCyc: 71% identical to serine hydroxymethyltransferase (Escherichia coli K-12 substr. MG1655)
4.1.2.-; Glycine hydroxymethyltransferase. [EC: 2.1.2.1]; RXN-6321 [EC: 2.1.2.1]; RXN0-5240 [EC: 2.1.2.1]

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

Sequence Analysis Tools

See A0A166NR87 at UniProt or InterPro

Protein Sequence (417 amino acids)

>Pf1N1B4_2454 Serine hydroxymethyltransferase (EC 2.1.2.1) (Pseudomonas fluorescens FW300-N1B4)
MFSKQDQIKGYDDALLAAMNAEEQRQEDHIELIASENYTSKRVMEAQGSGLTNKYAEGYP
GKRYYGGCEHVDKVEALAIERAKQLFGADYANVQPHSGSSANSAVYLALLQAGDTILGMS
LAHGGHLTHGAKVSSSGKLYNAVQYGIDTKTGLIDYDEVERLAVECKPKMIVAGFSAYSK
TLDFPRFRQIADKVGALLFVDMAHVAGLVAAGLYPNPLPYADVVTTTTHKTLRGPRGGLI
LAKANEEIEKKLNAAVFPGAQGGPLMHVIAGKAVCFKEALEPGFKAYQQQVIDNAQAMAG
VFIKRGYDVVSGGTDNHLFLVSLIRQGLTGKEADAALGRAHITVNKNAVPNDPQSPFVTS
GLRIGTPAVTTRGFKVTQCVELAGWICDILDNLGDADVEANVAQQVAALCADFPVYR