Protein Info for GFF3563 in Variovorax sp. SCN45
Annotation: L-carnitine dehydratase/bile acid-inducible protein F
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: 36% identical to SCCT_CHLAA: Succinyl-CoA--D-citramalate CoA-transferase (Caur_2266) from Chloroflexus aurantiacus (strain ATCC 29366 / DSM 635 / J-10-fl)
KEGG orthology group: None (inferred from 96% identity to vpe:Varpa_5656)MetaCyc: 40% identical to succinate--lglutarate CoA-transferase (Agrobacterium fabrum C58)
Succinate--hydroxymethylglutarate CoA-transferase. [EC: 2.8.3.13]
Predicted SEED Role
"L-carnitine dehydratase/bile acid-inducible protein F (EC 2.8.3.16)" (EC 2.8.3.16)
MetaCyc Pathways
- L-lysine degradation X (4/6 steps found)
- oxalate degradation II (1/3 steps found)
- L-lysine degradation IV (2/5 steps found)
- superpathway of L-lysine degradation (12/43 steps found)
Isozymes
Compare fitness of predicted isozymes for: 2.8.3.16
Use Curated BLAST to search for 2.8.3.13 or 2.8.3.16
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
Find the best match in UniProt
Protein Sequence (374 amino acids)
>GFF3563 L-carnitine dehydratase/bile acid-inducible protein F (Variovorax sp. SCN45) MTQPQGALAGIRVLDISRILGGPYCGQILGDHGADVLKVEPPQGDDTRTWGPPFKEGVAS YYHGLNRNKRVQHLDFSTEEGRESLLALVAEADVLIENFKTGTMERWGIGYDTLSQRFPR LVWCRVSGFGADGPLGALPGYDAAVQAMTGIMSINGEADGGPLRVGLPVVDMVTGLNAVI GVLLALQERNRSGRGQFVEAALYDSGLSLLHPHAANWFMDGTEPRRTGNAHPNIYPYDAL ATGTDPVFVAVGNDRQFASLCRCIGLPELAEDPLYRSAGARSVHRDGLKQRLEAAMAAFD GRQLVEQLMAAGVPAAPVLPVDAALQHPHTLHREMVVEMPGGYRGIGAPVKLSRTPASYR HAPLTPGEAFLPQD