Protein Info for GFF3431 in Xanthobacter sp. DMC5
Annotation: Serine hydroxymethyltransferase 2
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: 73% identical to GLYA_RHOCS: Serine hydroxymethyltransferase (glyA) from Rhodospirillum centenum (strain ATCC 51521 / SW)
KEGG orthology group: K00600, glycine hydroxymethyltransferase [EC: 2.1.2.1] (inferred from 91% identity to xau:Xaut_0870)MetaCyc: 68% identical to serine hydroxymethyltransferase subunit (Hyphomicrobium methylovorum GM2)
Glycine hydroxymethyltransferase. [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)
- folate polyglutamylation (5/5 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 transformations I (10/13 steps found)
- photorespiration I (7/9 steps found)
- photorespiration III (7/9 steps found)
- glycine biosynthesis I (1/1 steps found)
- glycine betaine degradation I (6/8 steps found)
- photorespiration II (7/10 steps found)
- glycine betaine degradation III (4/7 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) (7/13 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
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 (424 amino acids)
>GFF3431 Serine hydroxymethyltransferase 2 (Xanthobacter sp. DMC5) MTFHVSPAPAGDTAVFDAIRAELRRQQDQIELIASENIVSEAVLKAQGSVLTNKYAEGLP GKRYYGGCEHVDVVEVIAIDRAKALFGAGYANVQPHSGAQANAAVLMATLKPGDTLLGMS LAAGGHLTHGAPPTLSGKWFNAIGYGVAPDTALIDYDAVERLALEHRPKLIIAGGSSYPR IIDFARFRAIADQVGALLMVDAAHYAGLIAAGAYPSPFPHAHVVTTTTHKTLRGPRGGLI LTNDEALAKKLNSAVFPGLQGGPLMHVIAAKAVAFGEALTPEFRTYAAQVVANARALAAR LSQRGAAIVSGGTDSHMVLVDLRPFGVTGKAAEAALERAGLTCNKNGIPFDPAKPAVTSG IRLGTPAGTTRGFGVAEFETVADLIADVLTGLAANGAEANGKAEVAARATVRDICTRFPL YAGM