Protein Info for PP_0302 in Pseudomonas putida KT2440

Updated annotation (from data): L-carnitine 3-dehydrogenase (EC 1.1.1.108)
Rationale: Specific phenotype: utilization of Carnitine
Original annotation: L-carnitine dehydrogenase

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

1 50 100 150 200 250 321 signal peptide" amino acids 1 to 27 (27 residues), see Phobius details PF02737: 3HCDH_N" amino acids 11 to 185 (175 residues), 138.6 bits, see alignment E=2.2e-44 PF00725: 3HCDH" amino acids 188 to 274 (87 residues), 55.6 bits, see alignment E=6.3e-19

Best Hits

Swiss-Prot: 100% identical to LCDH_PSEPK: L-carnitine dehydrogenase (lcdH) from Pseudomonas putida (strain ATCC 47054 / DSM 6125 / NCIMB 11950 / KT2440)

KEGG orthology group: K00074, 3-hydroxybutyryl-CoA dehydrogenase [EC: 1.1.1.157] (inferred from 100% identity to ppu:PP_0302)

MetaCyc: 84% identical to L-carnitine dehydrogenase (Pseudomonas aeruginosa PAO1)
Carnitine 3-dehydrogenase. [EC: 1.1.1.108]

Predicted SEED Role

No annotation

MetaCyc Pathways

KEGG Metabolic Maps

Isozymes

Compare fitness of predicted isozymes for: 1.1.1.157

Use Curated BLAST to search for 1.1.1.108 or 1.1.1.157

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

See Q88R32 at UniProt or InterPro

Protein Sequence (321 amino acids)

>PP_0302 L-carnitine 3-dehydrogenase (EC 1.1.1.108) (Pseudomonas putida KT2440)
MPFITEIKTFAALGSGVIGSGWVARALAHGLDVVAWDPAPGAEQALRKRVANAWPALEKQ
GLAPGASQDRLKFVATIEECVRNADFIQESAPERLDLKLDLHAKISAAAKPDAIIGSSTS
GLLPSEFYESSTHPERCVVGHPFNPVYLLPLVEIVGGSRTSPEAIEAAKTIYTALGMRPL
HVRKEVPGFIADRLLEALWREALHLVNDGVATTGEIDDAIRFGAGLRWSFMGTFLTYTLA
GGDAGMRHFMSQFGPALKLPWTYLPAPELTDKLIDDVVSGTSEQQGERSIAALERYRDDT
LLAVLEAVKSSKASHGLSFSD