Protein Info for DDA3937_RS15600 in Dickeya dadantii 3937
Annotation: serine hydroxymethyltransferase
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: 96% identical to GLYA1_PECAS: Serine hydroxymethyltransferase 1 (glyA1) from Pectobacterium atrosepticum (strain SCRI 1043 / ATCC BAA-672)
KEGG orthology group: K00600, glycine hydroxymethyltransferase [EC: 2.1.2.1] (inferred from 100% identity to ddc:Dd586_3081)MetaCyc: 91% 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)
- 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)
- 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)
- glycine betaine degradation III (4/7 steps found)
- formaldehyde assimilation I (serine pathway) (8/13 steps found)
- glycine betaine degradation I (4/8 steps found)
- glycine betaine degradation II (mammalian) (1/4 steps found)
- purine nucleobases degradation II (anaerobic) (13/24 steps found)
KEGG Metabolic Maps
- Cyanoamino acid metabolism
- Glycine, serine and threonine metabolism
- Methane metabolism
- One carbon pool by folate
Isozymes
No predicted isozymesUse Curated BLAST to search for 2.1.2.1
Sequence Analysis Tools
PaperBLAST (search for papers about homologs of this protein)
Search CDD (the Conserved Domains Database, which includes COG and superfam)
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
See E0SAY8 at UniProt or InterPro
Protein Sequence (417 amino acids)
>DDA3937_RS15600 serine hydroxymethyltransferase (Dickeya dadantii 3937) MLKREMNIADYDAELWQAMQQEVVRQEEHIELIASENYTSPRVMQAQGSQLTNKYAEGYP GKRYYGGCEYVDVVEQLAIDRAKELFGADYANVQPHSGSQANFAVYTALLLPGDTILGMN LAHGGHLTHGSPVNLSGKLYNVVPYGIDDSGKINYDEMAELARTHKPKMIVGGFSAYSGI VDWAKMREIADSIGAYLFVDMAHVAGLVAAGVYPNPVPHAHIVTTTTHKTLAGPRGGLIL AKGGDEDLYKKLNSAVFPGGQGGPLMHVIAGKAVALKEAMEPEFKTYQQQVAKNAKAMVE VFLSRGFNVVSGGTDNHLFLLDLVSKNLTGKEADAALGRANITVNKNSVPNDPKSPFVTS GIRIGTPAATRRGFKEAEVRELAGWICDVLDNINDEAVIERVKQKVLDICARFPVYA